GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruI in Shewanella loihica PV-4

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate 5208528 Shew_1039 phosphoenolpyruvate-protein phosphotransferase PtsP (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_07335
         (954 letters)



>lcl|FitnessBrowser__PV4:5208528 Shew_1039
           phosphoenolpyruvate-protein phosphotransferase PtsP
           (RefSeq)
          Length = 743

 Score =  329 bits (844), Expect = 4e-94
 Identities = 215/577 (37%), Positives = 317/577 (54%), Gaps = 21/577 (3%)

Query: 391 ATVMLAPESGSLIQAVAAAPGIAIGPAHIQVLQAIDYPL-----RGESAAIERERLQNAL 445
           A V  AP+   +    +AA G+ I  AH  VL   + PL     R +    E   L  AL
Sbjct: 159 AEVKSAPDK-CVYTGTSAASGVVI--AHAMVLGG-EIPLEQQGRRTKQVDEELLALSQAL 214

Query: 446 NQVRSDIQGLIER---AKAKAIREIFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVI 502
           +  R+ +  L +R      K ++ IF   Q +LDD  L  E    ++ G +A +A   V 
Sbjct: 215 DACRNTLSALSQRFDGENEKEVQSIFSALQLLLDDTSLGGEYGREIQAGWTAISAVSRVS 274

Query: 503 EAAAKEQEALQDALLAERAADLRDVGRRVLAQLCGVETPN-EPDQPYILVMDEVGPSDVA 561
                  + +QD  + ERA D+RD+G+RVL +L   +    E D P ILV  E   + +A
Sbjct: 275 LRYIDHFQQMQDPYMQERATDIRDLGQRVLRELIEPQKMQLELDVPVILVTKEATATMLA 334

Query: 562 RLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHV 621
                ++ GI+T  GG  +H+AI+ARA G+PA++G    +     G  L+L+  RG++ +
Sbjct: 335 EFPQHKLVGIVTELGGVNSHAAILARAFGVPAVIGVEGILNAGIDGKQLILNANRGQVLI 394

Query: 622 DPDAATLQRAKEERDTREQRLKVAAEQRHEPALTRDGHAVEVFANIGESAGVASAVEQGA 681
            P    +   +      +   K  AE+  +PA+T D   + ++ N G  + +AS + +GA
Sbjct: 395 SPTPTLIGEYRSLISAEKALQKRYAEELSKPAMTLDERRIHLYLNAGLLSSLASEIAEGA 454

Query: 682 EGIGLLRTELIFMAHSQAPDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAK 741
           +G+GL RTE+ FM  ++ P EA Q   YR+VL+   GRP+V+RTLDVGGDKPL Y PI  
Sbjct: 455 DGVGLYRTEIPFMLQTRFPSEAEQVEVYRQVLNAALGRPVVMRTLDVGGDKPLSYLPII- 513

Query: 742 EENPFLGVRGIRLTLQRPQVMEAQLRALLR-SADSRPLRIMFPMVGSVDEWRQARAMTER 800
           EENPFLG RGIRLTL  P++   QLRA+L  S     L I+ PMV  +DE  QA A  E+
Sbjct: 514 EENPFLGWRGIRLTLDHPELFLVQLRAMLNASGGGEQLHILLPMVCCLDEIDQAIAYLEQ 573

Query: 801 LRLEIPV---ADLQ---LGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHP 854
             LE+      DLQ   +GIM+EVP+       +AK VDF SVG+NDLTQY LA+DR +P
Sbjct: 574 AYLEVKQDVHPDLQRPKIGIMLEVPALLFQLEEVAKRVDFISVGSNDLTQYLLAVDRNNP 633

Query: 855 TLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSAR 914
            +S   D  HP +L+ +     A   +   + VCGELA +P+ V +LV +G  +LS++  
Sbjct: 634 RVSTLYDSYHPGILRALTQARLACREYRLPISVCGELAGEPMGVLLLVAMGYTQLSMNQG 693

Query: 915 SIAEVKARVRELSLAQVQTLAQAALAVGSADDVRALV 951
           S+A++   +R +S   +  L   AL++ +  +VR L+
Sbjct: 694 SLAKINYLIRRVSYQDLSELLAQALSLTNGFEVRELL 730


Lambda     K      H
   0.318    0.135    0.381 

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: 1178
Number of extensions: 62
Number of successful extensions: 5
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: 954
Length of database: 743
Length adjustment: 42
Effective length of query: 912
Effective length of database: 701
Effective search space:   639312
Effective search space used:   639312
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: 56 (26.2 bits)

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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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