Alignments for a candidate for ald-dh-CoA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Shewanella amazonensis SB2B

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate 6937537 Sama_1693 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)

Query= CharProtDB::CH_024820
         (891 letters)



>FitnessBrowser__SB2B:6937537
          Length = 867

 Score = 1340 bits (3467), Expect = 0.0
 Identities = 669/867 (77%), Positives = 762/867 (87%), Gaps = 4/867 (0%)

Query: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60
           M VTN  ELN LV RV KAQ ++AS++QEQVD+IFRAAALAAADARI LAKMA  E+ MG
Sbjct: 1   MTVTNTQELNELVARVAKAQAQFASYSQEQVDRIFRAAALAAADARIRLAKMAAEETRMG 60

Query: 61  IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120
           +VEDKVIKNHFASEYIYN YKDEKTCG+L+ED TFGTITIAEP+GIICGIVPTTNPTSTA
Sbjct: 61  VVEDKVIKNHFASEYIYNKYKDEKTCGILAEDATFGTITIAEPVGIICGIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180
           IFK+LISLKTRN IIFSPHPRAK +T  AA IVL AAIAAGAPKD+IGWID+PSV LSN 
Sbjct: 121 IFKALISLKTRNGIIFSPHPRAKVSTTTAARIVLDAAIAAGAPKDIIGWIDEPSVALSNQ 180

Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240
           LM H  INLILATGGPGMVKAAYSSGKPAIGVGAGNTP+VIDETADIKRAV+S+LMSKTF
Sbjct: 181 LMTHEKINLILATGGPGMVKAAYSSGKPAIGVGAGNTPIVIDETADIKRAVSSILMSKTF 240

Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300
           DNGV+CASEQ+VVVVD+VYDAV+ERF++HGGYLL  KE  A+Q VILK+G LNA IVGQ 
Sbjct: 241 DNGVVCASEQAVVVVDAVYDAVKERFSSHGGYLLSKKENAALQKVILKDGGLNADIVGQS 300

Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360
           A  IA +A   VP +TK+LIGEVT +DE E FAHEKLSP L MYRA +FE+A++KAE LV
Sbjct: 301 AATIAAMANIKVPAHTKVLIGEVTDIDEKEAFAHEKLSPLLGMYRAANFEEALDKAEALV 360

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

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

Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540
           RALIVTD+FLFNNGY D+   +LK+ G+ETEVF+EVEADPTL++VR GA++A SF+PDVI
Sbjct: 479 RALIVTDKFLFNNGYCDETIRILKSQGLETEVFYEVEADPTLAVVRAGAKVATSFQPDVI 538

Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600
           +ALGGGSPMDAAKI+WVMYEHP+  F +LALRFMDIRKRIYKFPK+G KA M+A+ TTSG
Sbjct: 539 VALGGGSPMDAAKIIWVMYEHPDVDFADLALRFMDIRKRIYKFPKLGAKAMMVAIPTTSG 598

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

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

Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780
           +CHSMAHKLG++FH+PHGLANALLI NVIR+NA D PTKQ AFSQYDRP+A  RYA IA 
Sbjct: 719 ICHSMAHKLGAEFHLPHGLANALLISNVIRFNATDLPTKQAAFSQYDRPKALCRYAAIAS 778

Query: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840
           HLGL+  G+   AK+E L+A +E LKA +GIP SI++AGV EADF+A +D+L+EDAFDDQ
Sbjct: 779 HLGLA--GNNDEAKVEALIAKIEELKAAIGIPVSIKDAGVNEADFMAKLDELAEDAFDDQ 836

Query: 841 CTGANPRYPLISELKQILLDTYYGRDY 867
           CTGANPRYPLISELKQ+L+D+++GR Y
Sbjct: 837 CTGANPRYPLISELKQLLIDSFHGRAY 863


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: 1822
Number of extensions: 64
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: 867
Length adjustment: 43
Effective length of query: 848
Effective length of database: 824
Effective search space:   698752
Effective search space used:   698752
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)
SQLite3 databases

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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