GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Shewanella loihica PV-4

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate 5209439 Shew_1910 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)

Query= CharProtDB::CH_024820
         (891 letters)



>FitnessBrowser__PV4:5209439
          Length = 872

 Score = 1323 bits (3425), Expect = 0.0
 Identities = 662/870 (76%), Positives = 754/870 (86%), Gaps = 5/870 (0%)

Query: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60
           M V+N  EL+ LVERV KAQ ++A+F+QEQVDKIFRAAALAAADARI LAKMA  E+GMG
Sbjct: 1   MTVSNQQELDQLVERVAKAQAQFANFSQEQVDKIFRAAALAAADARISLAKMAANETGMG 60

Query: 61  IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120
           ++EDKVIKNHFASEYIYN YKD+KTCG+L ED TFGTITIAEP+G+ICGIVPTTNPTSTA
Sbjct: 61  VLEDKVIKNHFASEYIYNKYKDDKTCGILEEDPTFGTITIAEPVGLICGIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180
           IFK+LISLKTRN IIFSPHPRAK +T  AA +VL+AA+ AGAPKD+IGWID+PSV LSN 
Sbjct: 121 IFKALISLKTRNGIIFSPHPRAKVSTTTAARLVLEAAVEAGAPKDIIGWIDEPSVALSNQ 180

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

Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300
           DNGV+CASEQ+VVVVD+VYDAV+ERFA+HGGY+L  KE KA+Q VILKNGALNA IVGQ 
Sbjct: 241 DNGVVCASEQAVVVVDAVYDAVKERFASHGGYMLSSKEAKAMQKVILKNGALNADIVGQS 300

Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360
           A  IA +A   VP +TK+LIG+ T + ESE FAHEKLSP LAMYRA DF+DA+ KAE LV
Sbjct: 301 AATIAAMANIKVPASTKVLIGQATEISESEAFAHEKLSPLLAMYRASDFDDALNKAEALV 360

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

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

Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540
           RALIVTD++LFNNGY D+   +LK+ G+ETEVF+EVEADPTL+IV +GA +A SF+PDVI
Sbjct: 479 RALIVTDKYLFNNGYCDETIKILKSQGLETEVFYEVEADPTLAIVNQGASVAKSFQPDVI 538

Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600
           IALGGGSPMDAAKI+WVMYEHPE  F +LALRFMDIRKRIYKFPK+G KAKM+A+ TTSG
Sbjct: 539 IALGGGSPMDAAKIIWVMYEHPEVDFADLALRFMDIRKRIYKFPKLGKKAKMVAIPTTSG 598

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

Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720
           AYVSV+A+E+SDGQALQAL LL +YLP SY  G++ PVARE+VH+ ATIAGIAFANAFLG
Sbjct: 659 AYVSVMANEYSDGQALQALDLLVKYLPDSYALGAQAPVAREKVHNGATIAGIAFANAFLG 718

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

Query: 781 HL---GLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAF 837
           HL   G +  G     K+E LL  ++ LK  +GIP SI+EAGV EADF A +D+L+EDAF
Sbjct: 779 HLKLKGATGEGISDEEKVEALLEKIDELKKTIGIPASIQEAGVNEADFFAKLDELAEDAF 838

Query: 838 DDQCTGANPRYPLISELKQILLDTYYGRDY 867
           DDQCTGANPRYPLI+ELK IL  ++YG+ Y
Sbjct: 839 DDQCTGANPRYPLIAELKAILTASFYGKKY 868


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: 1817
Number of extensions: 58
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: 872
Length adjustment: 43
Effective length of query: 848
Effective length of database: 829
Effective search space:   702992
Effective search space used:   702992
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