GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Acidovorax sp. GW101-3H11

Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Ac3H11_1480 Aldehyde dehydrogenase B (EC 1.2.1.22)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1480
          Length = 486

 Score =  329 bits (844), Expect = 1e-94
 Identities = 195/465 (41%), Positives = 267/465 (57%), Gaps = 4/465 (0%)

Query: 9   RNYIDGAFVES--AAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIE 66
           R YIDG +V++   A L V NPANGAL+  +P A A + + A+AAA  A   W  + A +
Sbjct: 15  RCYIDGQWVDADNGATLAVNNPANGALIGTIPNAGAAQTQTAIAAADRAFGPWKDRTAED 74

Query: 67  RAGHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEII 126
           RA  LRR    +      +A  +T EQGK  + A  E+ + A Y+++ AE ARR+ GE+I
Sbjct: 75  RARILRRWFELMLQHQEDLALIMTSEQGKPLAEARGEIAYAASYIEWFAEEARRIYGEVI 134

Query: 127 ASDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFE 186
            S    + I + R+P+GV A I PWNFP  +I RK+APAL  G TI+VKP+ +TP +   
Sbjct: 135 PSPWLDKRIVVTREPVGVCAAITPWNFPAAMITRKVAPALAAGCTIIVKPATQTPLSALA 194

Query: 187 FARLVAETDLPRGVFNVVCG-AGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTK 245
            A L A   +P GVF+V+ G A  +G  L++ P V  ++FTGS E G  + A  AP L K
Sbjct: 195 MAELAARAGVPAGVFSVITGDARPIGAELTASPVVRKLTFTGSTEIGRVLAAQCAPTLKK 254

Query: 246 LNLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAA 305
           ++LELGG AP IV  DADL+ AV     S+  N+GQ C CA R+ VQ  V + F E++A 
Sbjct: 255 MSLELGGNAPFIVFEDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGVYDAFAEKLAR 314

Query: 306 AMAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQP 365
            +AA + G  L E  VE GPLI+   L K++A V  A A+GA +VTGG      G  Y+P
Sbjct: 315 TVAALKVGHGL-EEGVEQGPLIDEASLTKVEALVADAKARGARVVTGGRRHALGGTFYEP 373

Query: 366 TVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHAL 425
           T+L     D R+ REEIFGPV P+       EAI +AND E+GL +  ++RD+ +     
Sbjct: 374 TILADITPDMRMAREEIFGPVAPLFRFHTEAEAIQMANDTEFGLAAYFYSRDVGRVWRVS 433

Query: 426 RELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHT 470
             L +G   IN            GV++SG+G     HG+ EY  T
Sbjct: 434 GALQYGMVGINAGVISTAVAPFGGVKQSGMGREGSVHGIEEYVDT 478


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: 558
Number of extensions: 21
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: 486
Length adjustment: 34
Effective length of query: 443
Effective length of database: 452
Effective search space:   200236
Effective search space used:   200236
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: 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:

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