Alignments for a candidate for putA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Caulobacter crescentus NA1000

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate CCNA_00846 CCNA_00846 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

Query= reanno::SB2B:6938573
         (1058 letters)



>FitnessBrowser__Caulo:CCNA_00846
          Length = 1029

 Score =  956 bits (2470), Expect = 0.0
 Identities = 529/1027 (51%), Positives = 673/1027 (65%), Gaps = 14/1027 (1%)

Query: 31   DEEAYLKELIALVPSSDEEIARITSRAHDLVAKVRQYEKKGLMVGIDAFLQQYSLETQEG 90
            DE A + +L+A  P S E+ A + + A  LV   R+  +K  +V  ++FLQ++SL T+EG
Sbjct: 14   DEAAVIADLLAAKPLSSEDRAAVRAEAEALVRGARRSVRKQGVV--ESFLQEFSLGTREG 71

Query: 91   IILMCLAEALLRIPDAETADALIADKLSGAKWDEHMSKSDSVLVNASTWGLMLTGKIVQL 150
            + LMCLAEALLR PD +T D LIA+K+  A W  H+  SDS+ VNASTWGLMLTGKIV+ 
Sbjct: 72   LALMCLAEALLRTPDDDTRDKLIAEKIGSADWASHLGGSDSLFVNASTWGLMLTGKIVEP 131

Query: 151  DKNLDGTPSNLLSRLVNRLGEPVIRQAMYAAMKIMGKQFVLGRTIEEGLKNAAEKRKLGY 210
            D+         + +L  RLGEPVIR A+  A++IMG+QFVLGRTIE  +K AA +   G 
Sbjct: 132  DETARNDMPGFIKKLAGRLGEPVIRAAVGQAIRIMGEQFVLGRTIEAAIKRAAAE---GD 188

Query: 211  THSYDMLGEAALTMKDADKYYRDYANAIQALGTAKFDESEAPRPTISIKLSALHPRYEVA 270
              S+DMLGE A T  DA +Y + YA+AI+ +G             +S+KLSAL PRYE  
Sbjct: 189  MCSFDMLGEGARTAADAARYEKAYADAIETVGKLSNGAGPEAGHGVSVKLSALCPRYEAT 248

Query: 271  NEDRVMTELYATLIKLIEQARSLNVGIQIDAEEVDRLELSLKLFKKLYQSDAAKGWGLLG 330
            +EDRV  ELY   ++L + A   N+   IDAEE DRL LSLKL  KL +      W  LG
Sbjct: 249  HEDRVWEELYPRTLRLAKIAARHNLNFTIDAEEADRLALSLKLLDKLCREPELGDWTGLG 308

Query: 331  IVVQAYSKRALPVLMWLTRLAKEQGDEIPLRLVKGAYWDSELKWAQQAGEAGYPLFTRKA 390
            + VQAY KR   V+  L  L++E G  + +RLVKGAYWDSE+K AQ AG   YP+FT K 
Sbjct: 309  LAVQAYQKRCGEVIARLKALSEETGRRLMVRLVKGAYWDSEIKRAQVAGRPDYPVFTTKP 368

Query: 391  ATDVSYLACARYLLSEATRGVIYPQFASHNAQTVAAITAMVGDR--KFEFQRLHGMGQEL 448
            ATD+SYL  A+ L+  A    +Y QFA+HNA T+AA+  M  +   K E QRLHGMG+ L
Sbjct: 369  ATDLSYLVNAKALIEAAPH--LYAQFATHNAHTLAAVVRMAKNTGVKIEHQRLHGMGEAL 426

Query: 449  YDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKLVDPKTPIESLVTHP 508
            Y          T+R YAP+G H+DLLPYLVRRLLENGANTSFVH L+D + P+E +VT P
Sbjct: 427  YKAADDLYDGITLRAYAPVGGHEDLLPYLVRRLLENGANTSFVHALLDERVPVEKVVTDP 486

Query: 509  LKTLQGYKTLANNKIVKPADIFGAERKNSKGLNMNIISESEPFFAALEKFKDTQWSAGPL 568
            + T++ +    + KI  P +++G  R NS GL++++ ++ E   AA+        SAGPL
Sbjct: 487  IDTVEAHPD-RHAKIPTPINVYGERRVNSAGLDLSVKADRERLSAAVAAQDGVTLSAGPL 545

Query: 569  VNGETLSGEVR-DVVSPYNTTLKVGQVAFANEATIEQAIAGADKAFASWCRTPVETRANA 627
            V G+ ++G     +++P N    VG V+ A  A I++A   A  A  +W R     RA  
Sbjct: 546  VGGKVVAGGAPLPLIAPANDQKTVGVVSEAQSAQIDEAFKLARAAQPAWDRAGGVARAQV 605

Query: 628  LQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMSKPELLPG 687
            L+ + D LE N E LIAL +REAGK++ DGI EVREAVDFCRYYA+ A+    + E+L G
Sbjct: 606  LRAMGDALEANIERLIALLSREAGKTLSDGIAEVREAVDFCRYYAMLAEDQFGEAEILKG 665

Query: 688  PTGELNELFLQGRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFRAVQ 747
            P GE N L L GRGVFVCISPWNFPLAIF GQ+AAALA GN V+AKPAEQT LI F AV+
Sbjct: 666  PVGETNSLRLAGRGVFVCISPWNFPLAIFTGQIAAALAAGNAVLAKPAEQTPLIAFEAVK 725

Query: 748  LAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDGAIIP 807
            L H AG+   +L  LPG G  VGA LTS E + GV FTG T TA  IN+ LA R G I+P
Sbjct: 726  LYHAAGLDPRLLALLPGRGETVGAALTSHEDLDGVAFTGGTDTAWRINQTLAARQGPIVP 785

Query: 808  LIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDVLKG 867
             IAETGG N M VD+T+Q EQV++DV+ SAF SAGQRCSALR+L+L  D A+ +++ LKG
Sbjct: 786  FIAETGGLNGMFVDTTAQREQVIDDVIVSAFGSAGQRCSALRLLFLPHDTADHIIEGLKG 845

Query: 868  AMDELTLGNPGSVKTDVGPVIDAAAKANLNAHIDHIKQVGRLIHQLSLPEGTENGHFVAP 927
            AMD L LG+P    TDVGPVIDA AK  L+ H+  +K   +++H L+ P G   G F AP
Sbjct: 846  AMDALVLGDPALAVTDVGPVIDAEAKDALDKHLVRLKSDAKVLHALAAPAG---GTFFAP 902

Query: 928  TAVEIDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLGIHSRNEGHALEVA 987
               EI +   L +E FGP+LHVVRYK   L+KV   + +  +GLTLGIHSR E  A +V 
Sbjct: 903  VLAEIPTADFLEREVFGPVLHVVRYKPENLEKVAGALAARRYGLTLGIHSRIESFAADVQ 962

Query: 988  DKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAIGG 1047
              V  GN Y+NR+  GAVVGVQPFGG+GLSGTGPKAGGPH L RF  E+  + NITA GG
Sbjct: 963  RLVPAGNAYVNRSMTGAVVGVQPFGGEGLSGTGPKAGGPHALLRFAVERALSVNITAQGG 1022

Query: 1048 NATLLSL 1054
            +  LL+L
Sbjct: 1023 DPALLNL 1029


Lambda     K      H
   0.317    0.134    0.380 

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: 2548
Number of extensions: 99
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: 1058
Length of database: 1029
Length adjustment: 45
Effective length of query: 1013
Effective length of database: 984
Effective search space:   996792
Effective search space used:   996792
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 (21.7 bits)
S2: 58 (26.9 bits)

Align candidate CCNA_00846 CCNA_00846 (proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase)
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.13248.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-186  606.8   1.5   1.9e-186  606.4   1.5    1.2  1  lcl|FitnessBrowser__Caulo:CCNA_00846  CCNA_00846 proline dehydrogenase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00846  CCNA_00846 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  606.4   1.5  1.9e-186  1.9e-186       1     496 [.     505    1008 ..     505    1012 .. 0.99

  Alignments for each domain:
  == domain 1  score: 606.4 bits;  conditional E-value: 1.9e-186
                             TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsea 71  
                                            ++yge r ns+G+dl+++   ++l++ + ++   +  a p+vg+k +a g   p+ +pa+ ++ vG vsea
  lcl|FitnessBrowser__Caulo:CCNA_00846  505 NVYGERRVNSAGLDLSVKADRERLSAAVAAQDGVTLSAGPLVGGKVVAGGAPLPLIAPANDQKTVGVVSEA 575 
                                            58********************************************************************* PP

                             TIGR01238   72 daaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdfl 142 
                                            + a+++ea + a aa + w       ra +l+++ d le ++  l+all reaGktls+ iaevreavdf+
  lcl|FitnessBrowser__Caulo:CCNA_00846  576 QSAQIDEAFKLARAAQPAWDRAGGVARAQVLRAMGDALEANIERLIALLSREAGKTLSDGIAEVREAVDFC 646 
                                            *********************************************************************** PP

                             TIGR01238  143 ryyakqvedvldeesaka.............lGavvcispwnfplaiftGqiaaalaaGntviakpaeqts 200 
                                            ryya  +ed+++e                  +G++vcispwnfplaiftGqiaaalaaGn+v+akpaeqt+
  lcl|FitnessBrowser__Caulo:CCNA_00846  647 RYYAMLAEDQFGEAEILKgpvgetnslrlagRGVFVCISPWNFPLAIFTGQIAAALAAGNAVLAKPAEQTP 717 
                                            ************98765579*************************************************** PP

                             TIGR01238  201 liaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvplia 271 
                                            lia +av+l + aG+ +  + llpGrGe+vGaalts+e + Gv+ftG t++a +in++la r+ + vp+ia
  lcl|FitnessBrowser__Caulo:CCNA_00846  718 LIAFEAVKLYHAAGLDPRLLALLPGRGETVGAALTSHEDLDGVAFTGGTDTAWRINQTLAARQGPIVPFIA 788 
                                            *********************************************************************** PP

                             TIGR01238  272 etGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlt 342 
                                            etGG n m vd+ta  eqv+ dv+ saf saGqrcsalr+l++ +d ad++++ +kGamd l++g p +  
  lcl|FitnessBrowser__Caulo:CCNA_00846  789 ETGGLNGMFVDTTAQREQVIDDVIVSAFGSAGQRCSALRLLFLPHDTADHIIEGLKGAMDALVLGDPALAV 859 
                                            *********************************************************************** PP

                             TIGR01238  343 tdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvv 413 
                                            tdvGpvidaeak+ l +h+ ++k+ ak ++ +   +      gtf ap+l e+   d l++evfGpvlhvv
  lcl|FitnessBrowser__Caulo:CCNA_00846  860 TDVGPVIDAEAKDALDKHLVRLKSDAKVLHALAAPA-----GGTFFAPVLAEIPTADFLEREVFGPVLHVV 925 
                                            ****************************99998777.....8***************************** PP

                             TIGR01238  414 rykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGp 484 
                                            ryk ++l+kv   + a+ ygltlG+hsrie+  + +++ + +Gn yvnr + GavvGvqpfGGeGlsGtGp
  lcl|FitnessBrowser__Caulo:CCNA_00846  926 RYKPENLEKVAGALAARRYGLTLGIHSRIESFAADVQRLVPAGNAYVNRSMTGAVVGVQPFGGEGLSGTGP 996 
                                            *********************************************************************** PP

                             TIGR01238  485 kaGGplylyrlt 496 
                                            kaGGp+ l r+ 
  lcl|FitnessBrowser__Caulo:CCNA_00846  997 KAGGPHALLRFA 1008
                                            ********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1029 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 16.51
//
[ok]

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

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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