GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_927
          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:

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