GapMind for catabolism of small carbon sources

 

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

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate BWI76_RS07610 BWI76_RS07610 choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS07610 BWI76_RS07610 choline
           dehydrogenase
          Length = 554

 Score =  377 bits (968), Expect = e-109
 Identities = 230/533 (43%), Positives = 310/533 (58%), Gaps = 12/533 (2%)

Query: 1   MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHT--PLGLAAILPTRHV 58
           M+FDY+I+GAGSAG VLA RL+ DP  TV LLEAG  D      T  P  LA  L  R  
Sbjct: 1   MQFDYIIIGAGSAGNVLATRLTEDPDTTVLLLEAGGPDYRFDFRTQMPAALAFPLQGRRY 60

Query: 59  NWAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDW-QALGNEGWGFDD 117
           NWA++T P+P +  R     RGK LGGSS INGM YIRG+  D ++W  A G E W + D
Sbjct: 61  NWAYETEPEPHMNHRRMECGRGKGLGGSSLINGMCYIRGNAMDLDNWASAPGLEHWSYLD 120

Query: 118 VLPYFRKSEMHHGGSSEYHGGDGELYVSPANR--HAASEAFVESALRAGHSYNPDFNGAT 175
            LPY+RK+E    G+++YHGGDG + V+   +  +    A +E+ ++AG+    D NG  
Sbjct: 121 CLPYYRKAETRDIGANDYHGGDGPVSVTTPKQGNNPLFHAMIEAGVQAGYPRTDDLNGYQ 180

Query: 176 QEGAGYYDVTIR-DGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIK 234
           QEG G  D T+   GRR STA  +L   R R NLT+ TH   + I+  GK+A GV+ L  
Sbjct: 181 QEGFGPMDRTVTPQGRRASTARGYLDQARARPNLTIRTHALTDHIIFAGKRAVGVEWLEG 240

Query: 235 GSRVHLRA--RKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHA 292
            S    +A   KEV+L AGA  SP +L  SG+GS   L    I+  H LPGVG+NLQDH 
Sbjct: 241 DSTAPSKATANKEVLLCAGAIASPQILQRSGVGSPELLRQFDISLVHALPGVGENLQDHL 300

Query: 293 DVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPD 352
           ++ L Y+  +   L  +L       K   ++     G  ASN  EAG F+++      P+
Sbjct: 301 EMYLQYECKEPVSLYPALQWW-NQPKIGAEWLFGGTGIGASNQFEAGGFIRSREAFAWPN 359

Query: 353 IQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDD 412
           IQ H +   ++ +       HGF CHV  +R  S G V L S DP + P I  N+++H+ 
Sbjct: 360 IQYHFLPVAINYNGSNAVKEHGFQCHVGSMRSPSRGHVRLKSRDPHQHPAILFNYMSHEQ 419

Query: 413 DVATLLKGYRITRDIIAQTPMASFGLRDMYSAGLH--NDEQLIELLRKRTDTIYHPIGTC 470
           D        RITR+I++Q  + ++  R++ S G+   +D +L E +R   +T +HP GTC
Sbjct: 420 DWQEFRDAIRITREIMSQPALDNYRGREI-SPGIECQSDAELDEFVRNHAETAFHPCGTC 478

Query: 471 KMGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
           KMG DEMAVVD + RVHG+EGLRVVDASIMP ++ GN NA  IMI E+ A+ I
Sbjct: 479 KMGYDEMAVVDGEGRVHGLEGLRVVDASIMPQIITGNLNATTIMIGEKMADAI 531


Lambda     K      H
   0.319    0.137    0.419 

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: 867
Number of extensions: 43
Number of successful extensions: 8
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: 526
Length of database: 554
Length adjustment: 35
Effective length of query: 491
Effective length of database: 519
Effective search space:   254829
Effective search space used:   254829
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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