Alignments for a candidate for drdehyd-beta in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Shewanella amazonensis SB2B

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate 6939346 Sama_3439 isoquinoline 1-oxidoreductase, beta subunit, putative (RefSeq)

Query= metacyc::MONOMER-20833
         (739 letters)



>FitnessBrowser__SB2B:6939346
          Length = 750

 Score =  286 bits (732), Expect = 3e-81
 Identities = 230/762 (30%), Positives = 356/762 (46%), Gaps = 61/762 (8%)

Query: 13  NLSRRRFLA--STAVGALVIGFGLPLGAGRVQAATSAERGTQ--VPAFLEIRPDGTVRLL 68
           N SRR  L     + GAL++G    LG   + AA +A  G +  +  F+ I  D  V L 
Sbjct: 9   NFSRRDVLKLFGASGGALMLGAS-GLGWSPMLAAQTAAFGDEQRLNLFIAIGEDNRVYLT 67

Query: 69  SPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMSY 128
               E GQG  T + Q++ +EL+AD    +V      + Y     G + T GS S+R  +
Sbjct: 68  CHRSEMGQGIRTGIVQVLADELEADWDKVVVVQGLADKRY-----GSQNTDGSRSIRKGF 122

Query: 129 PTMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVP 188
             MR +GA+AR ML QA A+ W VPV E+  +   V H  S + L YGELA +A  +P+P
Sbjct: 123 DKMREMGAMARHMLEQAAAESWQVPVSEVYAKAHAVHHKGSDKRLSYGELAMAAAKLPMP 182

Query: 189 DPASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVG 248
           D  ++TL+ P +F  IGK    +D  D   G+A+Y  D + + +++A +   P  G  + 
Sbjct: 183 DAKTLTLKTPDKFTQIGKGHTIVDMDDMLGGRAIYGADNRPEGLVYAVIARPPVFGSQLE 242

Query: 249 SLRNQSQVEGMKGVHSVHVLP-----------GAVAVVAERWWHAKRAVEAIQVDWQEAA 297
           SL + S    + GV  +  LP           G VAVVA   W A    +A+++ W ++A
Sbjct: 243 SL-DDSAARKVAGVLDIVTLPVPKGAPAFQPLGGVAVVASNTWSALEGRKALKLSWSKSA 301

Query: 298 ADSALRVMPADFSSDKHREFLAAQ-QGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNH 356
            D+         +S  + + L  + Q P +     G    +    K  V ATY   YL H
Sbjct: 302 NDT--------HNSKAYLDTLKQRVQEPGKVARELGSQPASWPEDK-MVSATYTVPYLAH 352

Query: 357 AQLEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHF 416
           A +EPP+ +A  + +G  E+W  +Q P   + ++A   G+D  ++ ++  LLGG FGR  
Sbjct: 353 APMEPPAVIASVDKNG-CELWASSQTPQSTQQNVAGMLGIDEDKVKVNVTLLGGGFGRKS 411

Query: 417 LYDSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEA 476
             D +    +A  ++  +++P+ + WSRE+E     L  ++   ++A +D+KG   A+  
Sbjct: 412 KPDFS---VEAAFISSKINKPVLVQWSREDELRNGYLHAISAQYYQACIDEKGKVQAM-- 466

Query: 477 VSATEGPT-EALAGKQGDKIDPTAVE-GLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGN 534
           +S T  P+  +      D   P  ++ G +   + I   R   +  +    +G+ RSV N
Sbjct: 467 LSRTAFPSIGSTFDSAVDTPQPFELDLGFTDIPWDINAVRCEAVKAETHTRIGWLRSVSN 526

Query: 535 SLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLTTLLQAA---GELSGGWKRGP--- 588
             + F   SF+DELA   G         LL    R+          G       R P   
Sbjct: 527 IQHGFGVGSFVDELAIANGKSCTAQWRELL-GKARVENFANQGFEYGNYGEEQSRHPVDV 585

Query: 589 ------------FTAED--GTRRARGVAMASPFGSHTAAIAEVSIENGKVKVHDIWQAID 634
                        TA+   G     G A+   F ++ A   +V +E  K+ V D    +D
Sbjct: 586 GRYLKLIDRAEALTAQKPAGKNEGWGFAIHRSFVAYAAVAIKVRLEGDKLTVVDAIALMD 645

Query: 635 PGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVRV 694
            G++VNP  V AQ+ GAV  GLS  L  E  +  G     N+  YP+L       +   +
Sbjct: 646 AGTVVNPDRVAAQMEGAVVFGLSLALFGEIDFDQGAVTQSNFHDYPLLRLPHCPPIATEI 705

Query: 695 VESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPLSRH 736
           + S    GG+GEP +P VAPA+ NA+    G+R R LPLS+H
Sbjct: 706 IASSAVPGGVGEPGVPPVAPALTNAIVAAGGKRYRELPLSKH 747


Lambda     K      H
   0.317    0.134    0.394 

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: 1222
Number of extensions: 64
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 739
Length of database: 750
Length adjustment: 40
Effective length of query: 699
Effective length of database: 710
Effective search space:   496290
Effective search space used:   496290
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: 55 (25.8 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:

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
the source code
instructions for running GapMind on your computer

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