GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS01620
          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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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