GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA 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)



>FitnessBrowser__Koxy:BWI76_RS17250
          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:

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