GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Pseudomonas fluorescens GW456-L13

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate PfGW456L13_927 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)

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



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_927 Omega-amino
           acid--pyruvate aminotransferase (EC 2.6.1.18)
          Length = 454

 Score =  883 bits (2281), Expect = 0.0
 Identities = 427/453 (94%), Positives = 442/453 (97%)

Query: 1   MTSKNPQTREWQTLSSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGL 60
           MTS NPQTREWQTLS++HHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGL
Sbjct: 1   MTSNNPQTREWQTLSNDHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGL 60

Query: 61  WCVAIGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGS 120
           WCVAIGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAI+DIAPEGMNHVFFTGS
Sbjct: 61  WCVAIGYGRDELADAASKQMRELPYYNLFFQTAHPPVLELAKAIADIAPEGMNHVFFTGS 120

Query: 121 GSEGNDTMLRMVRHYWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPG 180
           GSEGNDTMLRMVRHYWAIKGQPNKKVIISR NGYHGSTVAGASLGGMTYMHEQGDLPIPG
Sbjct: 121 GSEGNDTMLRMVRHYWAIKGQPNKKVIISRKNGYHGSTVAGASLGGMTYMHEQGDLPIPG 180

Query: 181 IVHIPQPYWFGEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPD 240
           IVHI QPYWF EGG+MTPEEFG+WAANQLEEKILE+GVD VGAFIAEPIQGAGGVIIPP+
Sbjct: 181 IVHIAQPYWFAEGGEMTPEEFGVWAANQLEEKILEVGVDNVGAFIAEPIQGAGGVIIPPE 240

Query: 241 SYWPRIKEILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGG 300
           +YWPRIKEILAKYDILFVADEVICGFGRTGEWFGSDFY LKPDMMTIAKGLTSGYIPMGG
Sbjct: 241 TYWPRIKEILAKYDILFVADEVICGFGRTGEWFGSDFYDLKPDMMTIAKGLTSGYIPMGG 300

Query: 301 LIVRDEVVEVLNEGGDFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKR 360
           LIVRDEVV+VLNEGGDFNHGFTYSGHPVAAAV LENIRILR+EKI+E V++ETAPYLQKR
Sbjct: 301 LIVRDEVVDVLNEGGDFNHGFTYSGHPVAAAVGLENIRILRDEKIVERVKSETAPYLQKR 360

Query: 361 LRELNDHPLVGEVRGVGLLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDT 420
           LRELNDHPLVGEVRGVGLLGAIELVQDKATR R+ GKGVGMICRQFCFDNGLIMRAVGDT
Sbjct: 361 LRELNDHPLVGEVRGVGLLGAIELVQDKATRKRFEGKGVGMICRQFCFDNGLIMRAVGDT 420

Query: 421 MIIAPPLVITKAEIDELVTKARKCLDLTLSALQ 453
           MIIAPPLVIT AEIDELVTKARKCLDLTLSAL+
Sbjct: 421 MIIAPPLVITPAEIDELVTKARKCLDLTLSALR 453


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: 881
Number of extensions: 29
Number of successful extensions: 1
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: 454
Length adjustment: 33
Effective length of query: 421
Effective length of database: 421
Effective search space:   177241
Effective search space used:   177241
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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