Alignments for a candidate for adh in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Shewanella oneidensis MR-1

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate 201293 SO2136 aldehyde-alcohol dehydrogenase (NCBI ptt file)

Query= CharProtDB::CH_018413
         (862 letters)



>FitnessBrowser__MR1:201293
          Length = 866

 Score = 1017 bits (2630), Expect = 0.0
 Identities = 499/864 (57%), Positives = 654/864 (75%), Gaps = 4/864 (0%)

Query: 1   MKVTTVKELDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMG 60
           M VT  ++LD  ++ +  AQ +++ +SQ  VD IFR AA+AA DARI LAK A  ET MG
Sbjct: 1   MTVTNAQKLDLMVERVARAQAEYASFSQAQVDAIFRAAALAAADARISLAKMAAAETRMG 60

Query: 61  LVEDKVIKNHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTT 120
           ++EDKVIKNHFA EYIYNKYKDEKTCGI+  +  +G   IAEP+G++  I+P TNPTST 
Sbjct: 61  VIEDKVIKNHFASEYIYNKYKDEKTCGILSEDPTFGTITIAEPVGIICGIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQY 180
           IFK+LISLKTRN I FSPHPRAK ST  AAK +LDAA+ +GAP++IIGWIDEPS+ L+  
Sbjct: 121 IFKALISLKTRNAIIFSPHPRAKVSTTTAAKLVLDAAIAAGAPKDIIGWIDEPSVALSNQ 180

Query: 181 LMQ--KADITLATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTY 238
           LM   K ++ LATGGP +VK+AYSSGKPAIGVG GNTP++IDE+A IK AVSSI++SKT+
Sbjct: 181 LMTHPKVNLILATGGPGMVKAAYSSGKPAIGVGAGNTPIVIDETADIKRAVSSILMSKTF 240

Query: 239 DNGVICASEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIFKDGSVNPKIVGQS 298
           DNGV+CASEQ+VIV+ SIY +VK+ F   G Y++   + + +++VI K+G +N  IVGQS
Sbjct: 241 DNGVVCASEQAVIVVDSIYEQVKERFATHGGYLLNAAQTEAMQQVILKNGGLNADIVGQS 300

Query: 299 AYTIAAMAGIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYEADNFDDALKKAVTLI 358
           A TIA MAGI+VP TT++LIGEVT + E E FAHEKLSP+L MY A +F+DA+ KA TL+
Sbjct: 301 AATIAQMAGIEVPHTTKVLIGEVTDISETEAFAHEKLSPLLGMYRAADFNDAVDKAETLV 360

Query: 359 NLGGLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLG 418
            LGG+GHTSG+Y D+    +++  F   MKT R  +N P SQG  GDLYNF++ PS TLG
Sbjct: 361 ALGGIGHTSGLYTDQDTQTERVKSFGFRMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420

Query: 419 CGFWGGNSVSENVGPKHLLNIKTVAERRENMLWFRVPHKVYFKFGCLQFALKDLKDLKKK 478
           CG WGGNS+SENVGP HL+N KTVA+R ENMLW ++P  +YF+ G L  AL++L D  KK
Sbjct: 421 CGSWGGNSISENVGPSHLINKKTVAKRAENMLWHKLPSSIYFRRGSLPIALEELSD--KK 478

Query: 479 RAFIVTDSDPYNLNYVDSIIKILEHLDIDFKVFNKVGREADLKTIKKATEEMSSFMPDTI 538
           RA IVTD   +N  Y D  +KIL+   ++ +VF +V  +  L T+++  +  +SF PD I
Sbjct: 479 RALIVTDPFLFNQGYCDETLKILKAQGLETEVFYEVEADPTLATVRQGAKVANSFKPDVI 538

Query: 539 IALGGTPEMSSAKLMWVLYEHPEVKFEDLAIKFMDIRKRIYTFPKLGKKAMLVAITTSAG 598
           IALGG   M +AK++WV+YEHP+V F DLA++FMDIRKRIY FPK+G KA +VAI T++G
Sbjct: 539 IALGGGSPMDAAKIIWVMYEHPDVDFADLALRFMDIRKRIYKFPKMGVKATMVAIPTTSG 598

Query: 599 SGSEVTPFALVTDNNTGNKYMLADYEMTPNMAIVDAELMMKMPKGLTAYSGIDALVNSIE 658
           +GSEVTPFA+VTD  TG KY +ADY++TPNMAIVD  L+M MPK LTA+ GIDA+ +++E
Sbjct: 599 TGSEVTPFAVVTDEQTGKKYPIADYQLTPNMAIVDPNLVMDMPKSLTAFGGIDAITHALE 658

Query: 659 AYTSVYASEYTNGLALEAIRLIFKYLPEAYKNGRTNEKAREKMAHASTMAGMASANAFLG 718
           AY SV A+EY++G AL+A+ L+ KYLP+AY+ G  +  AREK+ + +T+AG+A ANAFLG
Sbjct: 659 AYVSVMANEYSDGQALQALDLLCKYLPDAYQLGAASPIAREKVHNGATIAGIAFANAFLG 718

Query: 719 LCHSMAIKLSSEHNIPSGIANALLIEEVIKFNAVDNPVKQAPCPQYKYPNTIFRYARIAD 778
           +CHSMA KL +E ++  G+ANALLI  VI+FNA D P KQA   QY  P  + RYA IAD
Sbjct: 719 ICHSMAHKLGAEFHLAHGLANALLISNVIRFNATDLPTKQAAFSQYDRPKALCRYAAIAD 778

Query: 779 YIKLGGNTDEEKVDLLINKIHELKKALNIPTSIKDAGVLEENFYSSLDRISELALDDQCT 838
           ++ LGGN+D +KV+ L+ KI +LKK L IP SI++AGV E +F + LD ++E A DDQCT
Sbjct: 779 HLALGGNSDAQKVEKLLEKIEQLKKTLGIPASIQEAGVNEADFLAKLDMLAEDAFDDQCT 838

Query: 839 GANPRFPLTSEIKEMYINCFKKQP 862
           GANPR+PL SE+K++ ++ +  +P
Sbjct: 839 GANPRYPLISELKQLLLDSYYGRP 862


Lambda     K      H
   0.317    0.134    0.378 

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: 1701
Number of extensions: 67
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: 862
Length of database: 866
Length adjustment: 42
Effective length of query: 820
Effective length of database: 824
Effective search space:   675680
Effective search space used:   675680
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: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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