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_RS25110 AZOBR_RS25110 (Fe-S)-binding protein

Query= uniprot:E4PLR6
         (483 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS25110 AZOBR_RS25110
           (Fe-S)-binding protein
          Length = 474

 Score =  511 bits (1316), Expect = e-149
 Identities = 261/467 (55%), Positives = 321/467 (68%), Gaps = 7/467 (1%)

Query: 9   ELTPDFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAGALS 68
           E + +F   +  AL D QLR NFR AMD LM+KRA  F D  E  G+R LG  ++  ALS
Sbjct: 3   ETSINFAKASSAALQDQQLRGNFRRAMDGLMSKRAVQFADTAEWNGVRTLGASVRLRALS 62

Query: 69  RLPDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMND 128
           +LP+LLE+LE   T+NG++VHWA T +EAN++V  I++      VVKGKSMVSEEM +N 
Sbjct: 63  KLPELLEKLEANCTKNGIQVHWASTTDEANAIVLSIMQRVNAKLVVKGKSMVSEEMHLNA 122

Query: 129 YLAERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPE-TEDVNQ 187
           +L + G+E LESD+GEYIVQLD   PSHIIMPAIH N +Q++ LF  K+ E E TEDV Q
Sbjct: 123 FLEKHGIESLESDLGEYIVQLDEAMPSHIIMPAIHMNTKQIAHLFKQKIKEAEYTEDVAQ 182

Query: 188 LIQIGRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEK 247
           L  + RR LR+KF  ADVG+SGVN A+AETGTL LVENEGNGRMSTT PPVHIAV G+EK
Sbjct: 183 LTDLARRVLRKKFATADVGISGVNMAVAETGTLCLVENEGNGRMSTTVPPVHIAVMGLEK 242

Query: 248 VVPNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTGAFA 307
           VV  L DV P++SLLTRSA  QPITTYVN+IS PRK  E DGP E+HLV+LDNGR+G +A
Sbjct: 243 VVEKLEDVPPVISLLTRSATAQPITTYVNMISSPRKEGEKDGPNEIHLVILDNGRSGIYA 302

Query: 308 DAQMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPSAS 367
           D ++R TL CIRCGACMNHCPVYT+VGGH Y   YPGPIG I+ P + GL+K  + P A 
Sbjct: 303 DEELRNTLRCIRCGACMNHCPVYTKVGGHAYQAPYPGPIGSILMPQVEGLEKRGELPHAC 362

Query: 368 SLCGACGEVCPVKIPIPELLQRLRQENVKNPEQPQQVKGGGAKYSRTERWIWRGWQMLNT 427
           ++C AC E+CPVKIPI E++ RLR E V        V+G G+  S+ E  +W+GW M   
Sbjct: 363 TMCNACVEICPVKIPIVEIMGRLRSEAV---HPGDAVRGAGSHASKAEAMVWKGWSMTYA 419

Query: 428 RPALYRSFLWAATRFRALAPKK---AGPWTENHSAPVPARRSLHDLA 471
            P  Y+       +    AP        WT   + P  A R+LH LA
Sbjct: 420 SPLAYQFATALLAKLGNAAPASLPLLKEWTNVRAKPRFANRTLHALA 466


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: 605
Number of extensions: 25
Number of successful extensions: 6
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: 474
Length adjustment: 34
Effective length of query: 449
Effective length of database: 440
Effective search space:   197560
Effective search space used:   197560
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 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