GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Shewanella sp. ANA-3

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate 7024610 Shewana3_1788 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)

Query= CharProtDB::CH_024820
         (891 letters)



>FitnessBrowser__ANA3:7024610
          Length = 866

 Score = 1353 bits (3501), Expect = 0.0
 Identities = 677/869 (77%), Positives = 759/869 (87%), Gaps = 4/869 (0%)

Query: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60
           M VTN  EL+ +VERV KAQ EYASF+Q QVD IFRAAALAAADARI LAKMA AE+ MG
Sbjct: 1   MTVTNAQELDLMVERVAKAQAEYASFSQAQVDAIFRAAALAAADARISLAKMAAAETRMG 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 DNGVVCASEQAVIVVDSIYEQVKERFATHGGYLLNAAQTAAMQQVILKNGGLNADIVGQS 300

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

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

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

Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540
           RAL+VTDRFLFN GY D+   +LKA G+ETEVF+EVEADPTL+ VR+GA++ANSFKPDVI
Sbjct: 479 RALVVTDRFLFNQGYCDETLKILKAQGLETEVFYEVEADPTLATVRQGAKVANSFKPDVI 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 AYVSVMANEYSDGQALQALDLLCKYLPDAYQLGGASPIAREKVHNGATIAGIAFANAFLG 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 HLALD--GNSDAEKVEKLLEKIEQLKKTLGIPASIQEAGVNEADFLAKLDELAEDAFDDQ 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: 1852
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: 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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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