GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Desulfovibrio vulgaris Hildenborough

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase

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



>lcl|MicrobesOnline__882:208056 DVU2559
           adenosylmethionine--8-amino-7-oxononanoate
           aminotransferase
          Length = 542

 Score =  234 bits (596), Expect = 7e-66
 Identities = 141/447 (31%), Positives = 235/447 (52%), Gaps = 17/447 (3%)

Query: 7   QTREWQTLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIG 66
           +T   ++L + H   PF+  +      P II  A G +L D++GN+ LDG++ LW    G
Sbjct: 57  RTARLRSLDAAHVWHPFTQMRDWMGSEPCIIDAADGNHLIDTDGNRYLDGVSSLWTNVHG 116

Query: 67  YGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGND 126
           +    + +A  +Q+  + +  L       P +ELA  ++ IAP G+  VF++ SGS   +
Sbjct: 117 HRHPHIDEAIRRQLDRVAHSTLL-GLGGTPSIELAARLTAIAPAGLTRVFYSDSGSTAVE 175

Query: 127 TMLRMVRHYW--AIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHI 184
             L++   Y   A +G   +  +++  N YHG T+   SLGGM+  H      +   V  
Sbjct: 176 AALKIAFQYHRQAPEGDARRTRVMAFSNAYHGDTIGSVSLGGMSLFHGIYGPLLFDPVRA 235

Query: 185 PQPYWFGEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWP 244
           P P+ +    D+ PE  G+    ++E  +   G +     +   +QGA G+++ P  +  
Sbjct: 236 PAPHCYRCPADLRPETCGMACLGEVERLMRHHGHELCAVVVEPLVQGAAGMLVQPRGWLR 295

Query: 245 RIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVR 304
            ++++  ++ +  VADEV  GFG+TG  F  +  G+ PDM+ +AKG+T GY+P+   +V 
Sbjct: 296 GLRDLCDRHGVFMVADEVAVGFGKTGTMFACEQEGVVPDMLCLAKGITGGYLPLAATLVT 355

Query: 305 DEVVE-VLNEGGDFN---HGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKR 360
           + + +  L    DF    HG TY+G+ +A A AL ++ +  EE+ +E +R      L   
Sbjct: 356 EHIHDGFLGGYADFRTFFHGHTYTGNALACAAALASLDVFEEERTLETLRPR-IERLATL 414

Query: 361 LRELNDHPLVGEVRGVGLLGAIELVQDKATRARY-----VGKGVGMICRQFCFDNGLIMR 415
           L  LND P VG++R VG++  IELV D+ TR  Y     +G  V +  R+     G+I+R
Sbjct: 415 LAPLNDLPHVGDIRRVGVMTGIELVADRETRTPYRPEERIGHRVTLEARR----RGVIVR 470

Query: 416 AVGDTMIIAPPLVITKAEIDELVTKAR 442
            +GD M++ PPL IT+ E++ LV   R
Sbjct: 471 PLGDVMVLMPPLSITETELETLVHTVR 497


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: 639
Number of extensions: 33
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: 542
Length adjustment: 34
Effective length of query: 420
Effective length of database: 508
Effective search space:   213360
Effective search space used:   213360
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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