Alignments for a candidate for drdehyd-beta in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-beta in Shewanella loihica PV-4

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate 5209812 Shew_2265 aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding (RefSeq)

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



>FitnessBrowser__PV4:5209812
          Length = 747

 Score =  306 bits (784), Expect = 2e-87
 Identities = 242/763 (31%), Positives = 358/763 (46%), Gaps = 66/763 (8%)

Query: 13  NLSRRRFLASTAVGALVIGFGLPLGAGRVQ---AATSAERGTQVPAFLEIRPDGTVRLLS 69
           N SRR  L          G GL LGA  +     A +     ++  F+ I  D  V L  
Sbjct: 9   NFSRRDVLKLFGAA----GGGLALGASGLAWSPMALAQNGEARLNLFIAIGEDDRVYLTC 64

Query: 70  PFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAYVVMENGLRITGGSMSVRMSYP 129
              E GQG  T + Q++ +EL AD    +V      + Y     G + T GS S+R  + 
Sbjct: 65  HRSEMGQGIRTGIPQVLADELGADWDKVVVVQGLADKRY-----GSQNTDGSRSIRKGFD 119

Query: 130 TMRRLGALARAMLLQAGAKQWGVPVGELTTQPGRVVHAASGRSLGYGELASSALDMPVPD 189
            MR +GA+AR ML QA A++  VPV EL+T   +V H+ASGRSL +GELA +A  +P+P+
Sbjct: 120 KMREMGAMARTMLEQAAAERLKVPVAELSTADNKVTHSASGRSLSFGELAMAAAKLPLPE 179

Query: 190 PASITLRDPSQFRWIGKPVKRLDAYDKSTGKALYSIDLKVDNMLHAAVQHAPRLGMTVGS 249
              + L+    F  IGK    +D      G A Y  D+ ++NML+A++   P LG  V  
Sbjct: 180 VTGLKLKSAKAFTHIGKGHTIVDMEAILDGSAEYGYDIHLENMLYASIVRPPVLGSKVDK 239

Query: 250 LRNQSQVEGMKGVHSVHVLP-----------GAVAVVAERWWHAKRAVEAIQVDWQEAAA 298
           L +++    + GV  V  LP           G VAV+A   W A +  +A++V W ++  
Sbjct: 240 LDDKA-ARAVAGVVDVIPLPGHQGAPSFQPLGGVAVLATNSWSAAQGRKALKVSWSDSPN 298

Query: 299 DSALRVMPADFSSDKHREFLAAQQGPTRDDENEGDVAGALKGAKTQVEATYHNQYLNHAQ 358
           D          SS    +   A Q   +     G+ + +    KT +EA Y   YL HA 
Sbjct: 299 D-------GHDSSAYLAQLKRAVQKSGKPVRQLGEQSQSWPADKT-IEAVYSVPYLAHAM 350

Query: 359 LEPPSALARFNPDGTLEIWLPNQAPDMFRADIAKRTGLDPAQITLHSPLLGGFFGRHFLY 418
           +EPP+A A    D T EIW   Q P   +  +A   GL   Q+T+H  LLGG FGR    
Sbjct: 351 MEPPAAAASVT-DKTAEIWASTQTPQSAQGTVAAALGLQAEQVTVHVTLLGGGFGRKSKP 409

Query: 419 DSANPYPQAIALAKAVSRPIKLIWSREEEFLRDVLRPLAVVKFRAALDDKGLPVAIEAVS 478
           D      +A  L++   RP+K+ WSRE+E     L  ++   F+A + DK    A+EA+ 
Sbjct: 410 DFC---VEAALLSQKTGRPVKVCWSREDELQNGYLHAISAQYFKARVGDK----AVEAIL 462

Query: 479 ATEG-PTEALAGKQGDKIDPTAVE---GLSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGN 534
              G P+ +    +G   +P+A E   G      AI + R   +       +G+ RSV N
Sbjct: 463 QRTGFPSISSTFAEGVD-EPSASELDLGFVDVPLAIDSLRCESVKASAHTRIGWMRSVCN 521

Query: 535 SLNDFFYESFLDELADKGGHDPYELRLHLLRDNPRLT--------------------TLL 574
             + F    F+DELA+K G D Y +   LL  + + T                       
Sbjct: 522 IQHGFGIGVFVDELANKRGLDTYTMWRELLGKDRQETFSDQQFNYGNYGETLERHPVDTA 581

Query: 575 QAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIENGK-VKVHDIWQAI 633
           +  G +S   +     A+    +  G A+   F ++ AA + V +   K +KV     AI
Sbjct: 582 RYKGVISAVEQEVKQMAKPEAGQGWGFAVHRSFTAYVAAASLVEVTQDKQLKVLKTVIAI 641

Query: 634 DPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPILAPAQMARVHVR 693
           D G++VNP  V +Q+ GAV  GLS  L+    + DG+    N+  YP+L  +Q   +   
Sbjct: 642 DAGTLVNPDRVASQLEGAVMFGLSIALMGRISFKDGRVEQSNFHDYPLLRMSQCPEIETI 701

Query: 694 VVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPLSRH 736
           +V S     G+GEP +P +AP++ NA+   +G R+R LPLS H
Sbjct: 702 LVPSMAPPAGVGEPGVPPIAPSIVNAIYAASGTRIRDLPLSDH 744


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: 1187
Number of extensions: 67
Number of successful extensions: 8
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: 739
Length of database: 747
Length adjustment: 40
Effective length of query: 699
Effective length of database: 707
Effective search space:   494193
Effective search space used:   494193
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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Protein sequences (fasta format)
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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