GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Desulfacinum infernum DSM 9756

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate WP_084076256.1 BUB04_RS06460 aspartate aminotransferase family protein

Query= reanno::pseudo3_N2E3:AO353_08585
         (454 letters)



>NCBI__GCF_900129305.1:WP_084076256.1
          Length = 449

 Score =  267 bits (682), Expect = 6e-76
 Identities = 158/433 (36%), Positives = 244/433 (56%), Gaps = 17/433 (3%)

Query: 19  HLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAASK 78
           H+     ++ LK+  P ++   +GVY+WD  G + +DG  G   V+IG+G  E+ +A  +
Sbjct: 5   HMKDHIFYRNLKKTYP-VVDRGEGVYIWDKNGKRYIDGSGGACVVSIGHGVPEILEAMKE 63

Query: 79  QMRELPYYNLFFQTAHPPVLELAKAISDIAPE-GMNHVFFTGSGSEGNDTMLRMVRHYWA 137
           Q R + + +    T+    LE A+ +  +AP+  +N V+F   GSE  +T +++VR YW 
Sbjct: 64  QARRICFAHGSHFTSEA-ALECAERLVRMAPDPALNRVYFLSGGSEAVETAVKVVRQYWR 122

Query: 138 IKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDMT 197
             G+P+K  +ISR   +HG+T    +LGG T   +          HI   Y +       
Sbjct: 123 EVGKPDKYKVISRWTSFHGNTTGALALGGHTGRRKHYHPLFLHTPHIEPAYCYRCPFGRE 182

Query: 198 PEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGA-GGVIIPPDSYWPRIKEILAKYDIL 256
           PE   +  A+QLE  I   G D V AFIAEP+ GA  G ++P D YW RI+EI   Y + 
Sbjct: 183 PEACSLECADQLERTIKYEGPDAVAAFIAEPVVGATAGALVPRDGYWQRIREICNAYQVK 242

Query: 257 FVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEG-G 315
            +ADEV+ G GRTG+ F  D + + PD++  AKGL+SGY P+G +IV++E+ + +  G G
Sbjct: 243 LIADEVMTGVGRTGQNFCLDHWKVVPDVIVTAKGLSSGYTPLGAVIVKEEIHDAIRSGSG 302

Query: 316 DFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAE-TAPYLQKRLRELNDHPLVGEVR 374
            F HG TY  +P++AA+    +R L E+ ++   R+E     L ++L+ L +HP VG+VR
Sbjct: 303 AFVHGHTYCQNPLSAAIGAAVLRYLEEQNLV--ARSERMGKVLLEKLQVLLEHPTVGDVR 360

Query: 375 GVGLLGAIELVQDKATRARY-VGKGVGMICRQFCFDNGLIM--------RAVGDTMIIAP 425
           G+GL   +ELV+DK T+A +     +     Q  F  GLI            GD +++AP
Sbjct: 361 GLGLFAGVELVRDKKTKATFDPSLKINARVAQEAFRRGLITYPGSGGADGIHGDHILLAP 420

Query: 426 PLVITKAEIDELV 438
           P VIT+++ID+LV
Sbjct: 421 PFVITESQIDDLV 433


Lambda     K      H
   0.320    0.140    0.428 

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: 590
Number of extensions: 35
Number of successful extensions: 7
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: 454
Length of database: 449
Length adjustment: 33
Effective length of query: 421
Effective length of database: 416
Effective search space:   175136
Effective search space used:   175136
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 Apr 09 2024. 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