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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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