GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS24850
          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:

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