Alignments for a candidate for ald-dh-CoA in Photobacterium jeanii R-40508

GapMind for catabolism of small carbon sources

Alignments for a candidate for ald-dh-CoA in Photobacterium jeanii R-40508

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_068329124.1 A3K86_RS06055 bifunctional acetaldehyde-CoA/alcohol dehydrogenase

Query= CharProtDB::CH_024820
         (891 letters)



>NCBI__GCF_001650345.1:WP_068329124.1
          Length = 900

 Score = 1391 bits (3601), Expect = 0.0
 Identities = 693/896 (77%), Positives = 786/896 (87%), Gaps = 8/896 (0%)

Query: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60
           M VTNVAEL+A++ RVK AQ+E+A+F+QE+VD IFRAA+LAA +ARIPLA+ AVAESGMG
Sbjct: 1   MPVTNVAELDAMIARVKAAQKEFATFSQEKVDAIFRAASLAANNARIPLAQQAVAESGMG 60

Query: 61  IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120
           IVEDKVIKNHFASE+IYN YKDE+TCG+L EDD  GT+TIAEP+GIICGIVPTTNPTSTA
Sbjct: 61  IVEDKVIKNHFASEFIYNKYKDEQTCGILEEDDNLGTMTIAEPVGIICGIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180
           IFKSLISLKTRNAIIFSPHPRAK++TN AA +VL AAIAAGAPKD+IGWIDQPSVELSNA
Sbjct: 121 IFKSLISLKTRNAIIFSPHPRAKNSTNDAAKLVLDAAIAAGAPKDIIGWIDQPSVELSNA 180

Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240
           LM H DINLILATGGPGMVKAAYSSGKPAIGVGAGN PVVIDETADIKRAVASVLMSKTF
Sbjct: 181 LMKHDDINLILATGGPGMVKAAYSSGKPAIGVGAGNVPVVIDETADIKRAVASVLMSKTF 240

Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300
           DNGV+CASEQ+V+V+D VYD V+ RFA+H GY+L   E + V+ V+L NGALNA IVGQP
Sbjct: 241 DNGVVCASEQAVIVMDEVYDEVKARFASHNGYVLTKSEAEKVRKVLLINGALNADIVGQP 300

Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360
           A KIAE+AG  VP NTKILIGE   V   + FAHEKLSPTL M+RA  FE+AV++A K+V
Sbjct: 301 ATKIAEMAGVKVPANTKILIGEGEEVCVEDEFAHEKLSPTLGMFRASSFENAVDQAVKMV 360

Query: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420
            +GGIGHTS LYT+QD    R+ YFG K+KTARIL+N P + GGIGDLYNF +APSLTLG
Sbjct: 361 ELGGIGHTSGLYTNQDVNADRIRYFGDKLKTARILVNIPTTHGGIGDLYNFNVAPSLTLG 420

Query: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480
           CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIA+ ++  +G K
Sbjct: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIAMSDL--EGKK 478

Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540
           RA +VTDRFLFNNGYAD++ S+LKA G+E + FF+VEADPTLS+V KGAE   SF+PDVI
Sbjct: 479 RAFLVTDRFLFNNGYADEVVSLLKAQGIEVQTFFDVEADPTLSVVEKGAEAMKSFQPDVI 538

Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600
           +ALGGGSPMDAAKIMWVMYEHPETHF ELA+RFMDIRKRIYKFPKMG KA+++ +TTTSG
Sbjct: 539 LALGGGSPMDAAKIMWVMYEHPETHFAELAMRFMDIRKRIYKFPKMGKKAELVCITTTSG 598

Query: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660
           TGSEVTPFAVVTDD TG KYPLADY +TP+MAIVDANLVM+MPKSL AFGG DAVTHA+E
Sbjct: 599 TGSEVTPFAVVTDDKTGAKYPLADYEITPNMAIVDANLVMNMPKSLTAFGGYDAVTHALE 658

Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720
           AYVSVLA+E+SDGQALQALK+LKEYLP+SY  G+ +P+ARE+VH+AATIAGIAFANAFLG
Sbjct: 659 AYVSVLANEYSDGQALQALKMLKEYLPSSYANGAADPIAREKVHNAATIAGIAFANAFLG 718

Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780
           VCHSMAHKLG++FH+PHGLANALLI NV+RYNANDNPTKQTAFSQYDRPQARRRYAE+AD
Sbjct: 719 VCHSMAHKLGAEFHLPHGLANALLISNVVRYNANDNPTKQTAFSQYDRPQARRRYAEVAD 778

Query: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840
           HLGLS  GDRTA KIE+LLAWLE LK  L IP SI+ AGV EADFLA +D+LS +AFDDQ
Sbjct: 779 HLGLSHEGDRTAQKIERLLAWLEELKVNLEIPTSIQAAGVPEADFLAKLDELSVEAFDDQ 838

Query: 841 CTGANPRYPLISELKQILLDTYYGRDYVEGET------AAKKEAAPAKAEKKAKKS 890
           CTGANPRYPLI+ELK +L+ +YYG+ +VEGET        K E A  +   KAKKS
Sbjct: 839 CTGANPRYPLITELKDVLVASYYGKAFVEGETFEGTTVIKKSEQAAEEKAPKAKKS 894


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: 2015
Number of extensions: 66
Number of successful extensions: 2
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: 900
Length adjustment: 43
Effective length of query: 848
Effective length of database: 857
Effective search space:   726736
Effective search space used:   726736
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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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
the source code
instructions for running GapMind on your computer

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