Aligments for a candidate for ald-dh-CoA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Aligments for a candidate for ald-dh-CoA 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_024820
         (891 letters)



>FitnessBrowser__MR1:201293
          Length = 866

 Score = 1352 bits (3500), Expect = 0.0
 Identities = 677/869 (77%), Positives = 760/869 (87%), Gaps = 4/869 (0%)

Query: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60
           M VTN  +L+ +VERV +AQ EYASF+Q QVD IFRAAALAAADARI LAKMA AE+ MG
Sbjct: 1   MTVTNAQKLDLMVERVARAQAEYASFSQAQVDAIFRAAALAAADARISLAKMAAAETRMG 60

Query: 61  IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120
           ++EDKVIKNHFASEYIYN YKDEKTCG+LSED TFGTITIAEP+GIICGIVPTTNPTSTA
Sbjct: 61  VIEDKVIKNHFASEYIYNKYKDEKTCGILSEDPTFGTITIAEPVGIICGIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180
           IFK+LISLKTRNAIIFSPHPRAK +T  AA +VL AAIAAGAPKD+IGWID+PSV LSN 
Sbjct: 121 IFKALISLKTRNAIIFSPHPRAKVSTTTAAKLVLDAAIAAGAPKDIIGWIDEPSVALSNQ 180

Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240
           LM HP +NLILATGGPGMVKAAYSSGKPAIGVGAGNTP+VIDETADIKRAV+S+LMSKTF
Sbjct: 181 LMTHPKVNLILATGGPGMVKAAYSSGKPAIGVGAGNTPIVIDETADIKRAVSSILMSKTF 240

Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300
           DNGV+CASEQ+V+VVDS+Y+ V+ERFATHGGYLL   + +A+Q VILKNG LNA IVGQ 
Sbjct: 241 DNGVVCASEQAVIVVDSIYEQVKERFATHGGYLLNAAQTEAMQQVILKNGGLNADIVGQS 300

Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360
           A  IA++AG  VP  TK+LIGEVT + E+E FAHEKLSP L MYRA DF DAV+KAE LV
Sbjct: 301 AATIAQMAGIEVPHTTKVLIGEVTDISETEAFAHEKLSPLLGMYRAADFNDAVDKAETLV 360

Query: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420
           A+GGIGHTS LYTDQD Q  RV  FG +MKTARILINTPASQGGIGDLYNFKLAPSLTLG
Sbjct: 361 ALGGIGHTSGLYTDQDTQTERVKSFGFRMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420

Query: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480
           CGSWGGNSISENVGP HLINKKTVAKRAENMLWHKLP SIYFRRGSLPIAL+E+     K
Sbjct: 421 CGSWGGNSISENVGPSHLINKKTVAKRAENMLWHKLPSSIYFRRGSLPIALEEL--SDKK 478

Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540
           RALIVTD FLFN GY D+   +LKA G+ETEVF+EVEADPTL+ VR+GA++ANSFKPDVI
Sbjct: 479 RALIVTDPFLFNQGYCDETLKILKAQGLETEVFYEVEADPTLATVRQGAKVANSFKPDVI 538

Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600
           IALGGGSPMDAAKI+WVMYEHP+  F +LALRFMDIRKRIYKFPKMGVKA M+A+ TTSG
Sbjct: 539 IALGGGSPMDAAKIIWVMYEHPDVDFADLALRFMDIRKRIYKFPKMGVKATMVAIPTTSG 598

Query: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660
           TGSEVTPFAVVTD+ TG+KYP+ADY LTP+MAIVD NLVMDMPKSL AFGG+DA+THA+E
Sbjct: 599 TGSEVTPFAVVTDEQTGKKYPIADYQLTPNMAIVDPNLVMDMPKSLTAFGGIDAITHALE 658

Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720
           AYVSV+A+E+SDGQALQAL LL +YLP +Y  G+ +P+ARE+VH+ ATIAGIAFANAFLG
Sbjct: 659 AYVSVMANEYSDGQALQALDLLCKYLPDAYQLGAASPIAREKVHNGATIAGIAFANAFLG 718

Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780
           +CHSMAHKLG++FH+ HGLANALLI NVIR+NA D PTKQ AFSQYDRP+A  RYA IAD
Sbjct: 719 ICHSMAHKLGAEFHLAHGLANALLISNVIRFNATDLPTKQAAFSQYDRPKALCRYAAIAD 778

Query: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840
           HL L   G+  A K+EKLL  +E LK  LGIP SI+EAGV EADFLA +D L+EDAFDDQ
Sbjct: 779 HLALG--GNSDAQKVEKLLEKIEQLKKTLGIPASIQEAGVNEADFLAKLDMLAEDAFDDQ 836

Query: 841 CTGANPRYPLISELKQILLDTYYGRDYVE 869
           CTGANPRYPLISELKQ+LLD+YYGR + E
Sbjct: 837 CTGANPRYPLISELKQLLLDSYYGRPFTE 865


Lambda     K      H
   0.317    0.132    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: 1847
Number of extensions: 63
Number of successful extensions: 3
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: 891
Length of database: 866
Length adjustment: 43
Effective length of query: 848
Effective length of database: 823
Effective search space:   697904
Effective search space used:   697904
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: 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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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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