GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Frischella perrara PEB0191

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_039105833.1 FPB0191_RS10160 bifunctional acetaldehyde-CoA/alcohol dehydrogenase

Query= CharProtDB::CH_024820
         (891 letters)



>NCBI__GCF_000807275.1:WP_039105833.1
          Length = 890

 Score = 1339 bits (3465), Expect = 0.0
 Identities = 670/889 (75%), Positives = 762/889 (85%), Gaps = 5/889 (0%)

Query: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60
           MAVT++ EL+ L+ RVK+AQ+ YA+FTQEQVDKIF AAA AAA ARIPLA+ AVAESGMG
Sbjct: 1   MAVTSLKELDELLVRVKQAQQVYATFTQEQVDKIFVAAATAAAAARIPLAQQAVAESGMG 60

Query: 61  IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120
           IVEDKVIKN FA+EYI N Y+++KTCG+++E+D FGTITIAEP+GIICGIVPTTNPTSTA
Sbjct: 61  IVEDKVIKNLFAAEYILNKYRNDKTCGIVAENDPFGTITIAEPLGIICGIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180
           IFKSLISLKTRNAI+FSPHPRAK +T +AA IVL AAI AGAPKD+IGWID+PS+ELSNA
Sbjct: 121 IFKSLISLKTRNAIVFSPHPRAKKSTIEAARIVLDAAIKAGAPKDIIGWIDEPSIELSNA 180

Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240
           LMHH DI  ILATGGPGMVKAAYSSGKPA+GVGAGNTPV+IDETAD+KRAVASVLMSKTF
Sbjct: 181 LMHHDDIAAILATGGPGMVKAAYSSGKPALGVGAGNTPVIIDETADLKRAVASVLMSKTF 240

Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKN-GALNAAIVGQ 299
           DNG+ICASEQ++VVVDSVYD VR     +G Y+L  KE KAVQ +IL + GALNA IVGQ
Sbjct: 241 DNGMICASEQAIVVVDSVYDEVRRLLTHYGAYVLNAKETKAVQGIILNDKGALNANIVGQ 300

Query: 300 PAYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKL 359
           PA KIAELAG  VP  +K+L+GEV+ VD SEPFAHEKLSPTLAM++AK FEDAV+KAEKL
Sbjct: 301 PATKIAELAGIKVPAGSKVLVGEVSKVDLSEPFAHEKLSPTLAMFKAKSFEDAVDKAEKL 360

Query: 360 VAMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTL 419
           V MGG+GHTS LYTDQD    R++YFG KMKT RILIN PA+ GGIGDLYNF LAPSLTL
Sbjct: 361 VEMGGLGHTSVLYTDQDRNRERITYFGSKMKTCRILINQPAAHGGIGDLYNFDLAPSLTL 420

Query: 420 GCGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGH 479
           GCGSWGGNS+SENVGPKHLINKK +AKRAENMLWHKLP SIYF+RGSLP+AL EVI  G 
Sbjct: 421 GCGSWGGNSVSENVGPKHLINKKVIAKRAENMLWHKLPSSIYFKRGSLPVALSEVIEQGA 480

Query: 480 KRALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDV 539
           KR  +VTD+FLFNNGY+ QIT  L+A GV  E FF+VEADPTLS+VRKG E  ++FKPD 
Sbjct: 481 KRVFVVTDKFLFNNGYSKQITDQLEAQGVICETFFDVEADPTLSVVRKGTESMSAFKPDT 540

Query: 540 IIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTS 599
           IIALGGGSPMDAAKIMWV+YEHPET F+ELALRFMDIRKR   FP MG KAK+I VTTTS
Sbjct: 541 IIALGGGSPMDAAKIMWVLYEHPETKFDELALRFMDIRKRTCHFPNMGEKAKLICVTTTS 600

Query: 600 GTGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAM 659
           GTGSEVTPFAVVTDDATGQKYPLADYA+TP+MAIVDANLVM MPKSLCA GG DAVTHA+
Sbjct: 601 GTGSEVTPFAVVTDDATGQKYPLADYAITPNMAIVDANLVMTMPKSLCAAGGYDAVTHAL 660

Query: 660 EAYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFL 719
           EAYVS++ASEFSDGQALQAL LLK YLPASY EG+ NP+ARE+VHSAAT+AG+AFA AFL
Sbjct: 661 EAYVSIMASEFSDGQALQALSLLKAYLPASYKEGANNPIAREKVHSAATLAGVAFAQAFL 720

Query: 720 GVCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIA 779
           GVCHSMAHK+G+ FHIPHG+ANA+LI NV+R+NA D PTKQ  FSQY  P+A  RYAEIA
Sbjct: 721 GVCHSMAHKIGAAFHIPHGVANAMLISNVVRFNATDKPTKQGTFSQYGHPKAVSRYAEIA 780

Query: 780 DHLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDD 839
           DHLGL++  D+   K+EKL+ WL+ L+ +L IP SI+E G+ E  FL+ VD+L+ DAFDD
Sbjct: 781 DHLGLTSASDKDDKKVEKLIGWLDQLRKDLDIPFSIKEFGIDEKLFLSQVDQLAVDAFDD 840

Query: 840 QCTGANPRYPLISELKQILLDTYYGRDYVE----GETAAKKEAAPAKAE 884
           QCTGANPRYPLI+ELKQILLDTYYGR Y +     E  A K AA   A+
Sbjct: 841 QCTGANPRYPLIAELKQILLDTYYGRPYQDKGDISEDVAIKTAAKGAAK 889


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: 1930
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: 890
Length adjustment: 43
Effective length of query: 848
Effective length of database: 847
Effective search space:   718256
Effective search space used:   718256
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 24 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