GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Shewanella oneidensis MR-1

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 202600 SO3497 aminotransferase, class III (NCBI ptt file)

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



>FitnessBrowser__MR1:202600
          Length = 446

 Score =  292 bits (748), Expect = 1e-83
 Identities = 169/435 (38%), Positives = 249/435 (57%), Gaps = 24/435 (5%)

Query: 15  SSEHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELAD 74
           S EH+  PF+  +Q K   PR++  A+G+Y  D  GNK+LD  AGLWC   G+GR E+++
Sbjct: 14  SLEHYWMPFTANRQFKAS-PRLLAQAEGMYYTDINGNKVLDSTAGLWCCNAGHGRREISE 72

Query: 75  AASKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRH 134
           A SKQ+R++ Y   F Q  HP   ELA+ +++++PEG+N VFFT SGSE  DT L+M   
Sbjct: 73  AVSKQIRQMDYAPSF-QMGHPIAFELAERLTELSPEGLNKVFFTNSGSESVDTALKMALC 131

Query: 135 YWAIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHE--QGDLPIPGIVHIP-----QP 187
           Y    GQ ++   I R  GYHG    G S+GG++   +   G L + G+ H+P     Q 
Sbjct: 132 YHRANGQASRTRFIGREMGYHGVGFGGISVGGLSNNRKAFSGQL-LQGVDHLPHTLDIQH 190

Query: 188 YWFGEGGDMTPEEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIK 247
             F  G        G   A  LE+ +   G + + A I EP+ G+ GVI+PP  Y  R++
Sbjct: 191 AAFSRG----LPSLGAEKAEVLEQLVTLHGAENIAAVIVEPMSGSAGVILPPQGYLKRLR 246

Query: 248 EILAKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEV 307
           EI  K+ IL + DEVI  FGR G  F S  +G+ PD++T AK + +G IPMG + V+D +
Sbjct: 247 EITKKHGILLIFDEVITAFGRVGAAFASQRWGVIPDIITTAKAINNGAIPMGAVFVQDYI 306

Query: 308 VEVLNEGG----DFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRE 363
            +   +G     +F HG+TYSGHPVAAA AL  + I + E++ E    E   Y ++ +  
Sbjct: 307 HDTCMQGPTELIEFFHGYTYSGHPVAAAAALATLSIYQNEQLFER-SFELERYFEEAVHS 365

Query: 364 LNDHPLVGEVRGVGLLGAIELVQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMII 423
           L   P V ++R  GL+   +L    A  ++ VGK  G    + CF  G ++RA GD + +
Sbjct: 366 LKGLPNVIDIRNTGLVAGFQL----APNSQGVGKR-GYSVFEHCFHQGTLVRATGDIIAM 420

Query: 424 APPLVITKAEIDELV 438
           +PPL++ K +ID++V
Sbjct: 421 SPPLIVEKHQIDQMV 435


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: 505
Number of extensions: 27
Number of successful extensions: 5
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: 446
Length adjustment: 33
Effective length of query: 421
Effective length of database: 413
Effective search space:   173873
Effective search space used:   173873
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