GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Klebsiella michiganensis M5al

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate BWI76_RS26000 BWI76_RS26000 aspartate aminotransferase family protein

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



>lcl|FitnessBrowser__Koxy:BWI76_RS26000 BWI76_RS26000 aspartate
           aminotransferase family protein
          Length = 406

 Score =  224 bits (571), Expect = 4e-63
 Identities = 146/409 (35%), Positives = 217/409 (53%), Gaps = 46/409 (11%)

Query: 23  IHPIFADS------AKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTH 76
           I PI+A +       K + V D +G+E++DFAGGIAV   GH HP ++AA+ EQ  KL H
Sbjct: 17  ILPIYAPAEFIPVKGKGSRVWDQQGKEYVDFAGGIAVTALGHCHPALVAALHEQGEKLWH 76

Query: 77  TCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATG------RA 130
           T   V   EP + L  K+   V   FA + + + +G+EA E A K+AR  T       + 
Sbjct: 77  TS-NVFTNEPALRLGRKL---VDATFADRVVFMNSGTEANETAFKLARHYTVTRHSPYKT 132

Query: 131 GVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS--IDDSIASI 188
            +IAF  A+HGR++ T+ + G+   YS G G  P  I    + N+LH V   +DD     
Sbjct: 133 KIIAFHNAFHGRSLFTVSVGGQP-KYSDGFGPKPADIVHVPF-NDLHAVKAVMDDHTC-- 188

Query: 189 ERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGR 248
                         A+++EP+QGEGG   A  EF++ LR LCDQH  LL+ DEVQ G GR
Sbjct: 189 --------------AVVVEPIQGEGGVTAATPEFLQGLRDLCDQHQALLVFDEVQCGMGR 234

Query: 249 TGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAA 308
           TG+ FA    GVT D+ T AK++ GGFP++ +    +   A   G  G TY G+P+ACA 
Sbjct: 235 TGSLFAYMHYGVTPDILTSAKALGGGFPISAMLTTHDIASAFHAGSHGSTYGGNPLACAV 294

Query: 309 ALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHK 368
             A  ++     +LD   A  E  V  L+ I A++ +  ++R +G +I  EL       K
Sbjct: 295 GGAAFDLINTPEVLDGVTAKRELFVQHLQQIDARFDLFSDIRGMGLLIGAEL-------K 347

Query: 369 PNAAAVAQ-VVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLA 416
           P     A+  +  A + G+++L+ G   +V+R +  L   D+ + +G+A
Sbjct: 348 PQYHGKARDFLYAAAEAGVMVLNAGP--DVMRFVPSLVIDDSDIAEGMA 394


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: 448
Number of extensions: 19
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: 406
Length adjustment: 31
Effective length of query: 394
Effective length of database: 375
Effective search space:   147750
Effective search space used:   147750
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 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, 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