GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Verminephrobacter eiseniae EF01-2

Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011812614.1 VEIS_RS24010 aldehyde dehydrogenase

Query= metacyc::MONOMER-16246
         (477 letters)



>NCBI__GCF_000015565.1:WP_011812614.1
          Length = 478

 Score =  620 bits (1600), Expect = 0.0
 Identities = 312/473 (65%), Positives = 376/473 (79%), Gaps = 3/473 (0%)

Query: 8   HRNYIDGAFV-ESAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIE 66
           ++NYIDG FV    A + V NPA+  L++ VP   A  V+ A++AAR AQ  W R PAI+
Sbjct: 5   YQNYIDGRFVPHRGATIAVHNPADHRLIAEVPDGDAAAVDAAVSAARRAQPAWERLPAIQ 64

Query: 67  RAGHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEII 126
           RAG+LR+I+ K+R  A  +A TI  EQGK+  LA VEVNFTADY+DYMAEWARRLEGE++
Sbjct: 65  RAGYLRQISVKLREHAEALATTIAREQGKVMPLARVEVNFTADYIDYMAEWARRLEGEVL 124

Query: 127 ASDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFE 186
            SDRP E++FL RKP+GV AGILPWNFPFFLIARKMAPAL+TGNT+V+KPSEETP N F 
Sbjct: 125 TSDRPNEHMFLLRKPIGVAAGILPWNFPFFLIARKMAPALITGNTVVIKPSEETPLNAFA 184

Query: 187 FARLVAETDLPRGVFNVVCGAG-QVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTK 245
           F +L+A+TDLP GVFN+V G G   G  L +H GV+LI+FTGSV TG RIM AAAPNLT+
Sbjct: 185 FTQLLAQTDLPPGVFNLVSGKGASTGAELVAHKGVNLITFTGSVTTGVRIMQAAAPNLTR 244

Query: 246 LNLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAA 305
           +NLELGGKAPAIVL DADL+LA +A+  SRIIN+GQVCNCAERVYVQR+V     ++I  
Sbjct: 245 VNLELGGKAPAIVLKDADLDLAAQALVASRIINTGQVCNCAERVYVQREVLGALTDKIVQ 304

Query: 306 AMAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAE-RPGHHYQ 364
            MAATR+G+PL +  ++MGPLIN+ GL+K+   V  A A GA ++TGG  A+   G+HY 
Sbjct: 305 RMAATRFGNPLLDETLDMGPLINQAGLDKVARLVDEARAAGAEVLTGGRRADVGHGYHYL 364

Query: 365 PTVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHA 424
           PTV+ GCR D  IMR+EIFGPVLP+Q VDD+DEAIALAND +YGLTSS+FTRDLN AM A
Sbjct: 365 PTVVAGCRQDMSIMRDEIFGPVLPLQAVDDMDEAIALANDSDYGLTSSIFTRDLNAAMKA 424

Query: 425 LRELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYLQS 477
            REL FGETYINREHFEAMQGFHAG +KSGIGGADG+HGL E+T THVVY+Q+
Sbjct: 425 CRELQFGETYINREHFEAMQGFHAGRKKSGIGGADGRHGLLEFTETHVVYMQT 477


Lambda     K      H
   0.320    0.136    0.395 

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: 658
Number of extensions: 23
Number of successful extensions: 4
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: 477
Length of database: 478
Length adjustment: 34
Effective length of query: 443
Effective length of database: 444
Effective search space:   196692
Effective search space used:   196692
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 (21.8 bits)
S2: 51 (24.3 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