Aligments for a candidate for lutB in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Aligments for a candidate for lutB in Azospirillum brasilense Sp245

Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate AZOBR_RS01620 AZOBR_RS01620 putative oxidoreductase subunit with NAD(P)-binding domain and ferridoxin-like domain

Query= uniprot:E4PLR6
         (483 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS01620 AZOBR_RS01620 putative
           oxidoreductase subunit with NAD(P)-binding domain and
           ferridoxin-like domain
          Length = 478

 Score =  349 bits (895), Expect = e-100
 Identities = 196/484 (40%), Positives = 269/484 (55%), Gaps = 36/484 (7%)

Query: 6   PVTELTPDFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAG 65
           P T   P+    A +AL+D +L+    +A    + +R  A     E E LR+ G  +K  
Sbjct: 3   PTTHAFPE---NARKALSDERLQKVLAIAPAGFVNRRKQAADRLPEFEDLRDQGRDLKNH 59

Query: 66  ALSRLPDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEME 125
            L+ L   LE  E K+ E G  VHW  T +EA   + GI        V KGKSM+SEE+ 
Sbjct: 60  VLANLDTYLEAFEGKVIEQGGHVHWCRTDQEARDAILGICRKVGAKTVTKGKSMISEEIG 119

Query: 126 MNDYLAERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFH----DKLGEPE 181
           +NDYL   G+  +E+D+GEYI+QL  E PSHII PA H +   V   F     D   +  
Sbjct: 120 INDYLEANGLTPIETDLGEYIIQLRREPPSHIIAPAFHLSKADVEGTFRQAHTDLPADRV 179

Query: 182 TEDVNQLIQIGRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIA 241
            ++   LI   R+ LRRKF +ADVG++G N  +AETG+ ++V NEGNG ++   P VH+ 
Sbjct: 180 LDEPKVLIAEARQVLRRKFQQADVGITGANIMVAETGSTVIVTNEGNGDLTQILPRVHVV 239

Query: 242 VTGIEKVVPNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNG 301
           +  I+KVVP L D   ++ LL RSA GQ  + Y    +GPR+P +LDGPEE H+VLLDNG
Sbjct: 240 IATIDKVVPTLEDAALVLRLLARSATGQEASAYTTFSTGPRRPGDLDGPEEFHVVLLDNG 299

Query: 302 RTGAFADAQMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVP 361
           R+ A    + +  L CIRCGACMNHCPVY  VGGH YG VYPGPIG ++ P + G+ +  
Sbjct: 300 RS-ALLGTEFQDVLRCIRCGACMNHCPVYGSVGGHAYGWVYPGPIGSVMQPALLGVKEAG 358

Query: 362 DHPSASSLCGACGEVCPVKIPIPELLQRLRQENVKNPEQPQQVKGGGAKYSRTERWIWRG 421
             P+AS+ CG C  VCP++IP+P++++  R++  +   QP  ++ G A        +W G
Sbjct: 359 HLPNASTFCGRCEAVCPMRIPLPKMMRHWREKEFEQNLQPAAMRRGLA--------LW-G 409

Query: 422 WQMLNTRPALYRSFLWAATRF--RALAPKKAGP-----------WTENHSAPVPARRSLH 468
           W     RPALY     AATR   RAL     G            WT +   P P  ++  
Sbjct: 410 W--FARRPALYH----AATRMAVRALGALGRGKGRFASLPLAQGWTRHRDMPAPEGKTFQ 463

Query: 469 DLAA 472
            + A
Sbjct: 464 QMWA 467


Lambda     K      H
   0.317    0.135    0.403 

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: 598
Number of extensions: 28
Number of successful extensions: 4
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: 483
Length of database: 478
Length adjustment: 34
Effective length of query: 449
Effective length of database: 444
Effective search space:   199356
Effective search space used:   199356
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: 51 (24.3 bits)

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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, 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

GapMind for catabolism of small carbon sources