GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Shewanella loihica PV-4

Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate 5209432 Shew_1903 para-aminobenzoate synthase, subunit I (RefSeq)

Query= curated2:P05378
         (462 letters)



>FitnessBrowser__PV4:5209432
          Length = 477

 Score =  233 bits (595), Expect = 8e-66
 Identities = 154/444 (34%), Positives = 228/444 (51%), Gaps = 23/444 (5%)

Query: 30  PVSFLLESVERGR-QSRFSIVGVGARRTFRLKDGVF-----------------TVNGERV 71
           P + LL+S       +R+ I+      T   +DGV                  + +G  +
Sbjct: 31  PWAILLDSAGADHIDARYDIISFDPLATITSQDGVTHTRHLRPTAASATEENQSKDGVEI 90

Query: 72  ETRDPLRALYERV--YAPLERHPDLPPFFGGVVGYAAYDLVRYYERLPSLKPDDLGLPDL 129
              DPL  L   +  Y P +   +LP F GG +G  +YDL R  E+LP++   D+ LP++
Sbjct: 91  SQDDPLSILQAAIADYFPTQHACELP-FSGGALGTFSYDLGRRIEKLPTIAAQDIELPEM 149

Query: 130 LFVEPEVVAVFDHLKNLLHLVAPGRDPEEAEARLFWAERRLKGPL-PGVPGERAGGRARF 188
                +   +F +      LV   R     + RL   E RL  P      GE+      +
Sbjct: 150 NIGLYDWALLFCYQSQTWSLVHY-RGETALKERLADLEARLSSPSNEKANGEKFALSRDW 208

Query: 189 QADFSREAYLEAVRRALDYIRAGDIFQVVLSLRLSSPLTVHPFALYRALRSVNPSPYMGY 248
           Q   ++  Y +   R  DY+ +GD +Q+ L+ R  +      +  Y  LR+ N +P+  +
Sbjct: 209 QPQITKGEYRDKFDRVQDYLHSGDCYQINLTQRFEAEYRGDEWQAYLKLRASNKAPFSAF 268

Query: 249 LDLGEVVLVSASPESLLRSDGRRVVTRPIAGTRPRGKDEEEDKRLAEELLRDEKEVAEHV 308
           + L    ++S SPE  ++  G  + T+PI GT  R  D   DK  AE L   EK+ AE++
Sbjct: 269 IRLDMHAILSISPERFIKLKGDAIETKPIKGTMARSSDATADKAAAEALAASEKDRAENL 328

Query: 309 MLLDLSRNDIGRVAAFGTVRVLEPLHVEHYSHVMHLVSTVEGILAEGKTPLDALASVLPM 368
           M++DL RNDIG+VA+ G+VRV     +E +  V HLVSTV   LA   +P D L +  P 
Sbjct: 329 MIVDLLRNDIGKVASPGSVRVPHLFAIESFPAVHHLVSTVTANLAAPNSPCDLLRAAFPG 388

Query: 369 GTVSGAPKIRAMEIIEELEPHRRGPYGGSFGYLAYDGAMDMALTLRTFVVAKGWMHVQAG 428
           G+++GAPKIRAMEIIEELEP RR  Y GS GY++ D  MD ++T+RT V     ++  AG
Sbjct: 389 GSITGAPKIRAMEIIEELEPSRRSLYCGSIGYISQDRQMDTSITIRTLVAEPPRLYCWAG 448

Query: 429 AGIVADSVPEREYEECWNKARALL 452
            GIVADS  + EY+E ++K   +L
Sbjct: 449 GGIVADSQVDAEYQESYDKVSKIL 472


Lambda     K      H
   0.321    0.139    0.408 

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: 499
Number of extensions: 18
Number of successful extensions: 2
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: 462
Length of database: 477
Length adjustment: 33
Effective length of query: 429
Effective length of database: 444
Effective search space:   190476
Effective search space used:   190476
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: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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:

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:

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:

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:

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