Alignments for a candidate for putA in Methylohalobius crimeensis 10Ki

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Methylohalobius crimeensis 10Ki

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_022948913.1 H035_RS0110405 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::ANA3:7023590
         (1064 letters)



>NCBI__GCF_000421465.1:WP_022948913.1
          Length = 1042

 Score =  951 bits (2457), Expect = 0.0
 Identities = 511/1034 (49%), Positives = 684/1034 (66%), Gaps = 19/1034 (1%)

Query: 27   KAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHELVNKVRQFDKKGLMVGIDAFLQ 86
            KA+   Y+ DE Q L  L+  V  SD A +RV  RA  LV  VRQ       + +DAFL 
Sbjct: 24   KAIAAAYLADEAQTLESLLPEVSLSDGARQRVHERARRLVQSVRQHP-----LPLDAFLS 78

Query: 87   QYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGAKWDEHLSKSDSVLVNASTWGL 146
            ++ L ++EG++LMCLAEALLRIPD  TA+ LI DKLS  KWD HL  S S LVNAST+GL
Sbjct: 79   EFELSSEEGVLLMCLAEALLRIPDDQTAERLIRDKLSRGKWDRHLGHSASFLVNASTFGL 138

Query: 147  MLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMAAMKIMGKQFVLGRTMKEALKN 206
            +LTG++++L+ +   T   L  +L+ R GE  +   ++ AMKI+G QF+L  T+++AL  
Sbjct: 139  LLTGRLMRLEIEDSDT---LFQKLLQR-GEAAVHVLVVRAMKILGGQFILATTIEKALA- 193

Query: 207  SEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITELGAQSYNENES-PRPTISIKL 265
               +R   + +S+DMLGE A T +D E YF  Y +AIT L     +E++    P IS+KL
Sbjct: 194  ---RRSPDFRYSFDMLGEEAFTAEDVEAYFRSYRHAITVLARHRGDESDVLAMPGISVKL 250

Query: 266  SALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISIDAEEVDRLELSLKLFQKLFNA 325
            SALHPRY     +RV  EL   ++ L K AR   IG+++DAEE +RL+L L +F+ +F  
Sbjct: 251  SALHPRYTFTQGERVRRELIPRLLTLAKEARAARIGLTLDAEEAERLDLMLDIFEAVFGH 310

Query: 326  DATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPVRLVKGAYWDSELKWAQQAGE 385
                 W   G+ VQAY KRA P++ +L  +A  QG  IPVRLVKGAYWD+E+K AQQ G 
Sbjct: 311  PDLSSWEGFGLAVQAYQKRAGPLIEYLRHIAASQGKRIPVRLVKGAYWDTEIKRAQQQGW 370

Query: 386  AAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASHNAQTVAAISDMAGDRNHEFQR 445
            + YP++TRK  TDVSYLA AR LL  A   A +PQFA+HNA TVA I ++A  R  EFQR
Sbjct: 371  SDYPVFTRKMNTDVSYLALARRLL--AFPRAFFPQFATHNAHTVAWILEVAEGRPLEFQR 428

Query: 446  LHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTP 505
            L GMG+ LY  +    G    R+YAP+G  ++LLPYL+RRLLENGANTSFVH+L D + P
Sbjct: 429  LQGMGEPLYRALRQTEGDIPCRVYAPVGGFRELLPYLMRRLLENGANTSFVHRLSDARLP 488

Query: 506  IESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRKNSKGLNMNIISEAEPFFAALDKFKS 565
            IE ++  P+  +   +T+ + +I  P D++   R NS G N++           L  F+ 
Sbjct: 489  IEEVIADPVAKVRTLETIPHPQIPQPADLYQPQRPNSPGPNLSDPLTYRRLNELLSSFRQ 548

Query: 566  TQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVAFADKAAIEQAVASADAAFATWTRTP 625
              W+A P V+G+   G+ + V SP D  Q VG V  A + +I +A+A A+AA   W R P
Sbjct: 549  NTWEAQPWVSGKGGEGKERMVYSPVDRGQVVGTVVEAGEESIAKALACAEAAAPEWDRVP 608

Query: 626  VEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKLMS 685
             E RA+ L++ A+L + +R+EL+ALC RE G+ + D +DEVREA+DF  YYA +A++L +
Sbjct: 609  AEDRAACLERAAELYQSHRDELLALCIREGGRCLSDAVDEVREAIDFLYYYAAEARRLFA 668

Query: 686  KPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQTSI 745
             P  LPGP GE N L+L GRG FVCISPWNFPLAIF GQ +AALAAGN V+AKPAEQT +
Sbjct: 669  NPLSLPGPVGESNRLYLHGRGPFVCISPWNFPLAIFTGQAAAALAAGNPVLAKPAEQTPL 728

Query: 746  IGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRTLAN 805
            I   A +L  QAGIP +VL +LPG G  VG AL  D RI GV FTGST TA  I R LA 
Sbjct: 729  IAALAARLLQQAGIPNEVLHFLPG-GGEVGAALVGDPRIRGVAFTGSTDTAWEIQRNLAG 787

Query: 806  REGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTSAGQRCSALRVLFLQEDIADR 865
            R   I   +AETGG NAM+VDS++ P+QVV DV++S+F SAGQRCSALR+LFLQ+++AD 
Sbjct: 788  RRAPIAAFVAETGGVNAMIVDSSALPQQVVADVLASTFNSAGQRCSALRILFLQDEVADP 847

Query: 866  VIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKANLDAHIDHIKQVGKLIKQMSLPAGTE 925
            V+D+L GA+ EL IG+P  + TD+GP+ID  A A L++H  +++   + + ++  P  T 
Sbjct: 848  VLDMLCGALAELKIGDPWDLSTDLGPLIDEDAVARLESHRAYLETNVQPLARLDPPPLT- 906

Query: 926  NGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTLGIHSRNE 985
             G +  P   EI +++ + +E FGPILHV+RY A  L  +++ I+  G+GLTLG+HSR +
Sbjct: 907  -GCYFGPAIYEITALEPVSREVFGPILHVMRYSAGHLDELLERIHGLGYGLTLGVHSRID 965

Query: 986  GHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTN 1045
                 +A+   VGN+Y+NRN IGAVVG  PFGG+GLSGTGPKAGGP+YL RF  EK+ + 
Sbjct: 966  AIWERIAEHARVGNIYVNRNMIGAVVGTHPFGGEGLSGTGPKAGGPNYLARFAYEKSLSV 1025

Query: 1046 NITAIGGNATLLSL 1059
            N  A+GG+  LLSL
Sbjct: 1026 NTAAVGGDPDLLSL 1039


Lambda     K      H
   0.317    0.133    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2442
Number of extensions: 95
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1064
Length of database: 1042
Length adjustment: 45
Effective length of query: 1019
Effective length of database: 997
Effective search space:  1015943
Effective search space used:  1015943
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.9 bits)

Align candidate WP_022948913.1 H035_RS0110405 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01238.hmm
# target sequence database:        /tmp/gapView.8532.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-185  603.4   0.0     2e-185  603.0   0.0    1.1  1  lcl|NCBI__GCF_000421465.1:WP_022948913.1  H035_RS0110405 bifunctional prol


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000421465.1:WP_022948913.1  H035_RS0110405 bifunctional proline dehydrogenase/L-glutamate gamma-semiald
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  603.0   0.0    2e-185    2e-185       1     496 [.     516    1018 ..     516    1022 .. 0.97

  Alignments for each domain:
  == domain 1  score: 603.0 bits;  conditional E-value: 2e-185
                                 TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGq 67  
                                                dly   r ns G +l+   + ++l+e l +  +++++a p v++k   eg+ + v +p+dr ++vG+
  lcl|NCBI__GCF_000421465.1:WP_022948913.1  516 DLYQPQRPNSPGPNLSDPLTYRRLNELLSSFRQNTWEAQPWVSGK-GGEGKERMVYSPVDRGQVVGT 581 
                                                799999************************************665.57888899************* PP

                                 TIGR01238   68 vseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiae 134 
                                                v ea ++ + +a+ +a aa++ew  ++a++raa+ler+a+l +sh  el+al++re G+ ls+a++e
  lcl|NCBI__GCF_000421465.1:WP_022948913.1  582 VVEAGEESIAKALACAEAAAPEWDRVPAEDRAACLERAAELYQSHRDELLALCIREGGRCLSDAVDE 648 
                                                ******************************************************************* PP

                                 TIGR01238  135 vreavdflryyakqvedvldeesaka.............lGavvcispwnfplaiftGqiaaalaaG 188 
                                                vrea+dfl yya +++  + +    +             +G++vcispwnfplaiftGq aaalaaG
  lcl|NCBI__GCF_000421465.1:WP_022948913.1  649 VREAIDFLYYYAAEARRLFANPLSLPgpvgesnrlylhgRGPFVCISPWNFPLAIFTGQAAAALAAG 715 
                                                *******************999777799*************************************** PP

                                 TIGR01238  189 ntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarli 255 
                                                n v+akpaeqt+liaa a  llq+aG+p  v+ +lpG Ge vGaal  d+ri+Gv+ftGst++a  i
  lcl|NCBI__GCF_000421465.1:WP_022948913.1  716 NPVLAKPAEQTPLIAALAARLLQQAGIPNEVLHFLPGGGE-VGAALVGDPRIRGVAFTGSTDTAWEI 781 
                                                ***************************************9.************************** PP

                                 TIGR01238  256 nkalakredapvpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrv 322 
                                                +++la r ++ ++++aetGG namivds+al++qvvadvlas+f+saGqrcsalr+l++q++vad v
  lcl|NCBI__GCF_000421465.1:WP_022948913.1  782 QRNLAGRRAPIAAFVAETGGVNAMIVDSSALPQQVVADVLASTFNSAGQRCSALRILFLQDEVADPV 848 
                                                ******************************************************************* PP

                                 TIGR01238  323 ltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfva 389 
                                                l+++ Ga+ elk+g p  l td+Gp+id++a  +l++h   ++++ + +a++          g +  
  lcl|NCBI__GCF_000421465.1:WP_022948913.1  849 LDMLCGALAELKIGDPWDLSTDLGPLIDEDAVARLESHRAYLETNVQPLARLDPPP----LTGCYFG 911 
                                                **************************************999998888877765554....789999* PP

                                 TIGR01238  390 ptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvG 456 
                                                p ++e+  l+ +++evfGp+lhv+ry a +ld+++++i   GygltlGvhsri+    +i ++a+vG
  lcl|NCBI__GCF_000421465.1:WP_022948913.1  912 PAIYEITALEPVSREVFGPILHVMRYSAGHLDELLERIHGLGYGLTLGVHSRIDAIWERIAEHARVG 978 
                                                ******************************************************************* PP

                                 TIGR01238  457 nvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrlt 496 
                                                n+yvnrn++GavvG  pfGGeGlsGtGpkaGGp yl r+ 
  lcl|NCBI__GCF_000421465.1:WP_022948913.1  979 NIYVNRNMIGAVVGTHPFGGEGLSGTGPKAGGPNYLARFA 1018
                                                **************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1042 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 13.14
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources