GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamD in Marinomonas arctica 328

Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate WP_111608784.1 DK187_RS18275 (Fe-S)-binding protein

Query= uniprot:Q39TW0
         (387 letters)



>NCBI__GCF_003259225.1:WP_111608784.1
          Length = 640

 Score =  187 bits (475), Expect = 7e-52
 Identities = 120/395 (30%), Positives = 190/395 (48%), Gaps = 51/395 (12%)

Query: 29  CYQCGLCDSVCPWNRVRQ-FSMRKIVRQGTFGLTE------------------------- 62
           C QCG C++VCP     Q  + +K+++    G                            
Sbjct: 248 CVQCGRCEAVCPAFAAGQPLNPKKLIQDMVVGFAGGTDENYAGSPYPGIDLGHAKGAPNQ 307

Query: 63  ------IEQEDIWRCSTCGTCPSRCPRGVNQIEAGVAMRR-IGAEYDVYPGH-VGTIRNV 114
                 I  + +W C+TC  C   CP  +  ++A V MRR +  E    P      + N+
Sbjct: 308 IITDGLIHPDTLWSCTTCRACVEECPMMIEHVDAIVDMRRFLTLEKGSTPNKGAQVLENI 367

Query: 115 VASLTSEGNSLGGDRTQRGDWAKD--LPVKPYAEGMELLYFTGCYLSYDPRMRKVAAATA 172
           +A+     N  G     R  WA D  LPV    +  ++L++     ++D R +++  A  
Sbjct: 368 IAT----DNPNGYAPASRTHWAADQNLPVMKDVKQADVLFWVSDG-AFDMRSQRILRAFV 422

Query: 173 AILNKAGVDFGILGSKESCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSPHCY 232
            ++  A VD  ILG +E   G+  R+ G++  F+ LAK N+         KI+ + PH +
Sbjct: 423 KLMKAANVDVAILGDEELDSGDVARRLGDDATFQSLAKRNLATLSTYQFNKIVTTDPHAF 482

Query: 233 HTFVNEYPEFKV----NFEVVFISQYIGQLINEGRLQITGEFAKKVTYHDPCYLGRHNGI 288
           H   NEY +F      N EV+  + ++ +L+ +G LQ+      KVTYHDPCYLGR+NG 
Sbjct: 483 HCLKNEYGDFGSDALQNVEVLHHTTFLNRLVKDGLLQLEPFKGGKVTYHDPCYLGRYNGE 542

Query: 289 YDEPRQVLQQVPGLELLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVDVGAT 348
           Y+ PR++L  + G+++ EM  ++  S CCGGGGG    + P E R AD+R+   V  GA+
Sbjct: 543 YEAPRELLASL-GIDVAEMERSKFRSRCCGGGGGAPITDIPGERRIADMRMEDVVSTGAS 601

Query: 349 VLATSCPYCITNFTDSSLDLADHEKVEVKDLAEII 383
           ++A  C  C      + L+     +  VKD+AEI+
Sbjct: 602 MVAVGCQQC-----TAMLEGVVEPRPVVKDIAEIL 631


Lambda     K      H
   0.320    0.139    0.427 

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: 581
Number of extensions: 34
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 387
Length of database: 640
Length adjustment: 34
Effective length of query: 353
Effective length of database: 606
Effective search space:   213918
Effective search space used:   213918
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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