Alignments for a candidate for gatA in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Shewanella oneidensis MR-1

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate 200074 SO0888 amidase family protein (NCBI ptt file)

Query= curated2:A7NKM0
         (490 letters)



>FitnessBrowser__MR1:200074
          Length = 568

 Score =  134 bits (336), Expect = 1e-35
 Identities = 157/558 (28%), Positives = 227/558 (40%), Gaps = 93/558 (16%)

Query: 1   MTPLYQLTVAQAREMLARGEISSLELTDALLTRIAA-----VEPKVRAFLVVDAAGARAQ 55
           M  + ++++A+ R  L  G  + +EL  + L R+AA      E K+ A LVV    A  +
Sbjct: 1   MFEVTEVSIAELRAALESGRTTVVELVKSYLARVAAYDGPATETKLNA-LVVHNPDALKE 59

Query: 56  ARAADARRAAGDA-SPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAA 114
           A A+DARRA G+  SPL GIP   KD    +GL     S   ++    YDA AV RL+AA
Sbjct: 60  AEASDARRARGETLSPLDGIPYTAKDSYLVKGLTAASGSPAFKDLVAQYDAFAVERLRAA 119

Query: 115 GAVILGKLNCDEFAMGSSTENSAFQQTRNPWNLERV----PGGSSGGSAAAVAAGEAPAA 170
           GA+ LGK N    A G   +   + +  +P+N E +      GSS G+    AA  +   
Sbjct: 120 GAICLGKTNMPPMANG-GMQRGHYGRAESPYNAEYLTAPFASGSSNGAGTGTAASYSAFG 178

Query: 171 LGTDTGGSIRQPAALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVI 230
           L  +T  S R PA+  G+    P+ G +S  G      ++D + P  RT+ D   VL VI
Sbjct: 179 LAEETWSSGRGPASNNGLCAYTPSRGVISVRGNWPLTPTMDVVVPYTRTMADMLEVLDVI 238

Query: 231 AGADP--------------FDATCTDYPAPDYEAALTGD-IRGLRIGVPREYF----VAG 271
              DP                   T  P      A + D ++G R GVPR Y     +AG
Sbjct: 239 VADDPITRGDLWRLQPWVQIPKASTVRPESYLALAASADTLKGKRFGVPRMYINKDELAG 298

Query: 272 MQP-------------------DVEAAVRTAIEVLREQGAEVCEISLP-------HTPYA 305
                                 D+  A R A+E     GAEV E+  P         P A
Sbjct: 299 TSENPGIGGPTGQRIHTRQSVIDLWEAARKALEA---AGAEVIEVDFPLVSNCEGDRPGA 355

Query: 306 LPVYY--LIAPAEASANLARFDGVRYG--LRVPGESYFDELERTRGAGFGPEVRRRIMLG 361
             V+   ++ P      L    G  +   LR   +   ++LE   G    P     +   
Sbjct: 356 PTVFNRGIVTPQFLHDELWELSGWAFDEFLRANNDPKLNKLEDVVGHLIFPHDLCTLPNR 415

Query: 362 TYALSAGY--YDAYYKRA-----------------QQVRTLIRRDYQQAFEQVDVIAAPT 402
              L+AG   Y    KR                  ++ R L   D+     ++D +  PT
Sbjct: 416 EGDLAAGMEEYVNMAKRGLKSFDQIDSIPDGLRGLEKTRKLDLEDWMDGL-KLDAVLFPT 474

Query: 403 TPTVAFKIGAHTDDPLA--MYLEDVCTLPLNLA----GLPGLVVPCGFAE--GLPIGLQL 454
              V     AH +   A   +   V     NLA    G+P + VP G     G+P+GL  
Sbjct: 475 VADVG-PADAHVNPASADIAWSNGVWVANGNLAIRHLGVPTVTVPMGVMADIGMPVGLTF 533

Query: 455 IGRAFDEESLLRVGDAYQ 472
            GRA+D+ +LL+   A++
Sbjct: 534 AGRAYDDNNLLKFAGAFE 551


Lambda     K      H
   0.320    0.136    0.398 

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: 607
Number of extensions: 30
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 490
Length of database: 568
Length adjustment: 35
Effective length of query: 455
Effective length of database: 533
Effective search space:   242515
Effective search space used:   242515
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis