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 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:

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