GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Klebsiella michiganensis M5al

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate BWI76_RS17250 BWI76_RS17250 bifunctional acetaldehyde-CoA/alcohol dehydrogenase

Query= CharProtDB::CH_024820
         (891 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS17250 BWI76_RS17250 bifunctional
           acetaldehyde-CoA/alcohol dehydrogenase
          Length = 891

 Score = 1691 bits (4380), Expect = 0.0
 Identities = 857/891 (96%), Positives = 879/891 (98%)

Query: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60
           MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG
Sbjct: 1   MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60

Query: 61  IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120
           IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA
Sbjct: 61  IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120

Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180
           IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA
Sbjct: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180

Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240
           LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF
Sbjct: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240

Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300
           DNGVICASEQSVVVVDSVYDAVRERF++HGGYLLQG+ELKAVQ++ILKNGALNAAIVGQP
Sbjct: 241 DNGVICASEQSVVVVDSVYDAVRERFSSHGGYLLQGQELKAVQNIILKNGALNAAIVGQP 300

Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360
           AYKIAELAGF+VP +TKILIGEVT VDESEPFAHEKLSPTLAMYRAK+FEDAV+KAEKLV
Sbjct: 301 AYKIAELAGFTVPVSTKILIGEVTDVDESEPFAHEKLSPTLAMYRAKNFEDAVDKAEKLV 360

Query: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420
           AMGGIGHTSCLYTDQDNQP RV+YFGQ MKTARILINTPASQGGIGDLYNFKLAPSLTLG
Sbjct: 361 AMGGIGHTSCLYTDQDNQPERVAYFGQLMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420

Query: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480
           CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK
Sbjct: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480

Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540
           RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTL+IVRKGAELANSFKPDVI
Sbjct: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLTIVRKGAELANSFKPDVI 540

Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600
           IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKM+A+TTTSG
Sbjct: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMVAITTTSG 600

Query: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660
           TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVM+MPKSLCAFGGLDAVTHA+E
Sbjct: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMEMPKSLCAFGGLDAVTHALE 660

Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720
           AYVSVLASEFSDGQALQALKLLKE LPASYHEGSKNPVARERVHSAATIAGIAFANAFLG
Sbjct: 661 AYVSVLASEFSDGQALQALKLLKENLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720

Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780
           VCHSMAHKLGSQFHIPHGLANALLI NVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD
Sbjct: 721 VCHSMAHKLGSQFHIPHGLANALLISNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780

Query: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840
           HLGL+APGDRTAAKIEKLL WL+ +KAELGIPKSIREAGVQEADFLA+VDKLSEDAFDDQ
Sbjct: 781 HLGLTAPGDRTAAKIEKLLGWLDEIKAELGIPKSIREAGVQEADFLAHVDKLSEDAFDDQ 840

Query: 841 CTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA 891
           CTGANPRYPLI+ELKQILLDT+YGR+YVEG    KKEAAPAKAEKKAKKSA
Sbjct: 841 CTGANPRYPLIAELKQILLDTFYGRNYVEGGVEEKKEAAPAKAEKKAKKSA 891


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: 2144
Number of extensions: 67
Number of successful extensions: 1
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: 891
Length adjustment: 43
Effective length of query: 848
Effective length of database: 848
Effective search space:   719104
Effective search space used:   719104
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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