GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Pedobacter sp. GW460-11-11-14-LB5

Align Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase

Query= SwissProt::Q6F9G0
         (483 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS24850 CA265_RS24850 aldehyde
           dehydrogenase
          Length = 454

 Score =  246 bits (628), Expect = 1e-69
 Identities = 143/448 (31%), Positives = 233/448 (52%), Gaps = 3/448 (0%)

Query: 30  IFNPATQELIGYVPNMGRAETERAIEAAYASWEMWKTKTAKERSALLKKWYDLILLNLDV 89
           I NPAT E+I  +     +  +   +A   +   W  KT +ER A++  + DL+ + ++ 
Sbjct: 3   IINPATAEIITSLEEDNLSTLQLKFDALQKAQPQWAGKTLQERIAVITHFSDLLEVEIEK 62

Query: 90  LAEILTTEQGKPFNEAKGEIIYAASFIEWFAEEAKRIYGDIIPSPYPDARIVVNKQPIGV 149
           LA +LT+E GKP  +++ EI  A + I+W    A++   D + +  P  + ++  +P+GV
Sbjct: 63  LASVLTSEVGKPLQQSRNEINGARARIKWMLANAEKYLADEVMTDEPGIKEIIKYEPLGV 122

Query: 150 VAAITPWNFPAAMITRKVAPALAAGCPCIVKPAPETPFTALALADLAIQAGIPAEIMSVV 209
           V  I+ WN+P  +      PAL +G   + KP+     T + +  L  +AG+P ++  + 
Sbjct: 123 VCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDDVFHIA 182

Query: 210 TGDAAQIGDAIFASDHVRKFTFTGSTPIGKLLLEKSAKTLKKVSLELGGNAPFIVFDDA- 268
            G A + G A+   D    F FTGS   GKL+ EK A  +    LELGG  P  + DD  
Sbjct: 183 IG-AKETGSALLNMDFNGYF-FTGSYKTGKLIYEKVAAKMVPCQLELGGKDPLYITDDVT 240

Query: 269 DIEAAVEGALIAKFRNAGQTCVCVNRFLVQSGVYEKFIQVFKAKIESLKIGNGLEAGSEI 328
           D+ AA  G     F N GQ+C  V R  VQ   Y+ +   F  +++S K G     G  I
Sbjct: 241 DVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAEGVYI 300

Query: 329 GPLINAQAVAKVQSHIEDALSKNGRLITGGQVHATGELFFEPTLIADANTEMMVATQETF 388
           G L   + ++ +++ ++DAL+K  +L+TGG+       +FEPT++ D   +M+V  +E+F
Sbjct: 301 GALTRKEQISVLENQVKDALNKGAKLLTGGKAVEGKGYYFEPTVLTDVTNDMLVMQEESF 360

Query: 389 GPLAAIFKFDTEQQAIQMANDTEFGLAAYCYTRDLGRAWRMSEQLEYGMVGINKGLISNE 448
           GP+  I K   + +A++M  DT++GL A  YT    RA ++  QL+ G    N     + 
Sbjct: 361 GPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCCDRVSA 420

Query: 449 VAPFGGIKHSGLGREGSKYGIEDYLEIK 476
             P+ G K+SG+G   S  GI  + + K
Sbjct: 421 ALPWSGRKYSGIGATLSHQGIRAFTKPK 448


Lambda     K      H
   0.319    0.135    0.397 

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: 462
Number of extensions: 17
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: 483
Length of database: 454
Length adjustment: 33
Effective length of query: 450
Effective length of database: 421
Effective search space:   189450
Effective search space used:   189450
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: 51 (24.3 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 preprint 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