Alignments for a candidate for put1 in Methylosarcina fibrata AML-C10

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Methylosarcina fibrata AML-C10

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_020563770.1 A3OW_RS0112455 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

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



>NCBI__GCF_000372865.1:WP_020563770.1
          Length = 1037

 Score =  945 bits (2443), Expect = 0.0
 Identities = 514/1040 (49%), Positives = 686/1040 (65%), Gaps = 19/1040 (1%)

Query: 24   ELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHELVNKVRQFDKKGLMVGIDA 83
            +L  A+  +Y+ DE+  ++EL++ + + D         A  LV  VR   K      I+A
Sbjct: 8    DLRAAINRSYLTDEKVIVNELLRNIGTYDPL--GAGELAGTLVTAVRA--KSHRNTAIEA 63

Query: 84   FLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGAKWDEHLSKSDSVLVNAST 143
            FL +Y L ++EG++LM +AEALLRIPD+ T D  +++KL+GA W+ HL +SDS+LV+ + 
Sbjct: 64   FLHEYQLNSREGVVLMGIAEALLRIPDSRTQDLFLQEKLTGADWNRHLLQSDSLLVHFTN 123

Query: 144  WGLMLTGKIV-KLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMAAMKIMGKQFVLGRTMKE 202
              L  T +   +L  K    P  +    ++RLG P+IR A+  AM+ + +QFV    M E
Sbjct: 124  KALSFTSEFEHRLLSKEHWLP--VFEEALSRLGAPLIRTAVKQAMRYLAQQFVFADAMPE 181

Query: 203  ALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITELGAQSYNENESPRPTIS 262
            AL+ SE+  +  +  S+DMLGEAA+T  DAE+Y+  Y +A+  L  +    +    P IS
Sbjct: 182  ALQISEEFPEERF--SFDMLGEAAVTAADAERYYQAYRHAVRTLAERENLADPQLNPGIS 239

Query: 263  IKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISIDAEEVDRLELSLKLFQKL 322
            IKLSAL PRYE     R + EL + +  L + AR   I +++DAEE +RL++SL +F  +
Sbjct: 240  IKLSALCPRYEPLQHRRAVGELSEKLRALAREARAAGIPMTVDAEESERLDMSLDVFAAV 299

Query: 323  FNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIPVRLVKGAYWDSELKWAQQ 382
            F+    KGW  LG+ VQAY KRALPVL WL  LA      +PVRLVKGAYWDSE+K AQ+
Sbjct: 300  FSHPDLKGWPGLGLAVQAYQKRALPVLRWLAALAASHRCRVPVRLVKGAYWDSEIKRAQE 359

Query: 383  AGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASHNAQTVAAISDMAGDRN-- 440
             G A YP++T K+ TDVSYLACA YLLS  +    YPQFA+HNA TVAAI   AG  +  
Sbjct: 360  NGLAGYPVFTHKSMTDVSYLACAHYLLSKTSE--FYPQFATHNAHTVAAILQ-AGKHHPG 416

Query: 441  HEFQRLHGMGQELYDTILSEAGAKA-VRIYAPIGAHKDLLPYLVRRLLENGANTSFVHKL 499
            +EFQRLHGMG+ LY  +++ +  K   R+YAP+G +++LLPYLVRRLLENGANTSF++++
Sbjct: 417  YEFQRLHGMGERLYREVMAVSERKIPCRVYAPVGDYRELLPYLVRRLLENGANTSFINQI 476

Query: 500  VDPKTPIESLVVHPLKTLTGYKTLANN-KIVLPTDIFGSDRKNSKGLNMNIISEAEPFFA 558
              P+  +  LV  P++T+   K+L    +IVLP D++G  R NS G+N+    +      
Sbjct: 477  DHPEWSVAELVRDPVETV---KSLPKTPQIVLPKDLYGERRPNSHGVNLADPFQLRQLQQ 533

Query: 559  ALDKFKSTQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVAFADKAAIEQAVASADAAF 618
             LD    TQW A P        G  + VV+P D   TVG V  A+ A +E+A+  A  AF
Sbjct: 534  ELDALAGTQWTAMPSGRKPLQAGAGRPVVNPCDNRLTVGSVGMAEPADVERALEKASHAF 593

Query: 619  ATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAV 678
              W  +    RA  L++  DLLE++R EL++LC RE G++++D + EVREAVD+CRYYA 
Sbjct: 594  NDWRLSSAATRAGCLRRAGDLLEQHRSELVSLCCREGGRTLRDALAEVREAVDYCRYYAQ 653

Query: 679  QAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAK 738
             A++L ++P LLPGPTGE N L+  GRGVFVCISPWNFP+AIF+GQ++AALAAGNTV+AK
Sbjct: 654  SAEELFAEPMLLPGPTGEENRLYYYGRGVFVCISPWNFPIAIFIGQMTAALAAGNTVIAK 713

Query: 739  PAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKL 798
            PA QT +     V+L HQAGIP  VLQ++P  G   G+ L AD R+ G+ FTGST TA+ 
Sbjct: 714  PASQTVLTAMLCVRLLHQAGIPEPVLQFVPAEGRLSGDLLVADPRVAGIAFTGSTDTAQW 773

Query: 799  INRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTSAGQRCSALRVLFL 858
            I+R LA +   +IPLIAETGGQN M+ DS++ PEQ+V DVV+S+F SAGQRCSALRVLF+
Sbjct: 774  IHRRLAQQHPMLIPLIAETGGQNVMIADSSALPEQLVQDVVASTFNSAGQRCSALRVLFV 833

Query: 859  QEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKANLDAHIDHIKQVGKLIKQM 918
            Q+DIAD++I +L GAM EL +G+P    TDVGPVID  A   L  H++ +++  +++ Q+
Sbjct: 834  QQDIADKIIGMLIGAMQELALGDPGRYATDVGPVIDRAALKPLAEHVEKMREQARMLYQL 893

Query: 919  SLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGLTL 978
             L      G F  PT +EI S+  L  E FGPILHVIRY+  EL  VI  IN TG+GLTL
Sbjct: 894  PLTEALSYGSFFPPTLIEIASLSQLTHEVFGPILHVIRYRGPELDRVIAAINETGYGLTL 953

Query: 979  GIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRFV 1038
            GIHSR E     +   V VGN+Y+NRN IGAVVGVQPFGG GLSGTGPKAGGP YL RF 
Sbjct: 954  GIHSRIEATVRAIRQGVRVGNIYVNRNMIGAVVGVQPFGGMGLSGTGPKAGGPDYLRRFA 1013

Query: 1039 TEKTRTNNITAIGGNATLLS 1058
             E+T   N  A+GGNA LL+
Sbjct: 1014 VEQTVATNTAAVGGNAGLLA 1033


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: 2385
Number of extensions: 92
Number of successful extensions: 8
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: 1037
Length adjustment: 45
Effective length of query: 1019
Effective length of database: 992
Effective search space:  1010848
Effective search space used:  1010848
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)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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