GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PV4:5208528
          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.

Links

Downloads

Related tools

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