GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Amantichitinum ursilacus IGB-41

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate WP_053937056.1 WG78_RS06780 aspartate aminotransferase family protein

Query= metacyc::MONOMER-11537
         (425 letters)



>NCBI__GCF_001294205.1:WP_053937056.1
          Length = 400

 Score =  233 bits (595), Expect = 6e-66
 Identities = 146/396 (36%), Positives = 217/396 (54%), Gaps = 34/396 (8%)

Query: 36  VTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKIN 95
           V D  G+E+IDF GGIAV + GH HP+++AA+TEQ NKL H    V   EP + L + + 
Sbjct: 31  VWDQAGKEYIDFGGGIAVNSLGHCHPELVAALTEQGNKLWHIS-NVFTNEPALALAKTL- 88

Query: 96  AKVPGDFAKKTLLVTTGSEAVENAVKIARAAT------GRAGVIAFTGAYHGRTMMTLGL 149
             V   FA++     +G+EA E A+K+AR A+       +  V++   ++HGRT  T+ +
Sbjct: 89  --VEHTFAERVFFCNSGAEANEAALKLARRASIEKYGERKNKVLSALNSFHGRTFFTVSV 146

Query: 150 TGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKNDAEPRDIAAIIIEPV 209
            G+   YS G G  P GI    Y          + +AS+E +  +D      A +IIEP+
Sbjct: 147 GGQP-KYSDGFGPKPAGIEHFKY----------NDLASLEALIDDDT-----ACVIIEPI 190

Query: 210 QGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGVTADLTTFAK 269
           QGEGG   A +EF++ +RALCD+   LLI DEVQ+G GRTG+ +A    GV  D+ + AK
Sbjct: 191 QGEGGVTPATQEFLQGVRALCDKFNALLIFDEVQSGNGRTGSLYAYMDFGVVPDILSTAK 250

Query: 270 SIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVG 329
            + GGFP+  +    +    +  G  G TY G+P+A A A   + +      L   KA  
Sbjct: 251 GLGGGFPIGAMLTTEKVAKHLVAGTHGTTYGGNPLATAVAGTAISIITRPETLSGVKAKS 310

Query: 330 ERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPNAAAVAQVVAKARDKGLILL 389
           ER+  GL+AI  KYPV+ E+R +G +I V+L          A     V+  A ++G+++L
Sbjct: 311 ERIRAGLQAIADKYPVVAEIRGMGLLIGVQL------KAEYAGRSRDVLNAAAEEGVLVL 364

Query: 390 SCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECFAEL 425
           + G   +V+R    L   D ++D GLA +E+ FA L
Sbjct: 365 AAGP--DVVRFAPSLVISDDEIDAGLARVEKAFARL 398


Lambda     K      H
   0.320    0.137    0.394 

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: 446
Number of extensions: 24
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: 425
Length of database: 400
Length adjustment: 31
Effective length of query: 394
Effective length of database: 369
Effective search space:   145386
Effective search space used:   145386
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: 50 (23.9 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