GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Shewanella loihica PV-4

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate 5208454 Shew_0966 beta alanine--pyruvate transaminase (RefSeq)

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



>FitnessBrowser__PV4:5208454
          Length = 446

 Score =  290 bits (741), Expect = 8e-83
 Identities = 165/433 (38%), Positives = 248/433 (57%), Gaps = 24/433 (5%)

Query: 17  EHHLAPFSDFKQLKEKGPRIITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAA 76
           EH+  PF+  +Q K+  PR++  A+G+Y  D  G  +LDG AGLWC   G+GR  +++A 
Sbjct: 16  EHYWMPFTANRQFKQS-PRLLAQAEGMYYKDVNGRPVLDGTAGLWCCNAGHGRKAISEAV 74

Query: 77  SKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYW 136
           SKQ+ E+ Y   F Q  HP   ELA+ ++ IAP+G+N VFFT SGSE  DT L++  +Y 
Sbjct: 75  SKQIHEMDYAPSF-QMGHPLAFELAERLAAIAPKGINKVFFTNSGSESVDTALKIALNYH 133

Query: 137 AIKGQPNKKVIISRINGYHGSTVAGASLGGM-----TYMHEQGDLPIPGIVHIPQPYWFG 191
             +G+  +   I R  GYHG    G S+GG+     T+  +     + G+ H+P      
Sbjct: 134 RARGEATRTRFIGRELGYHGVGFGGISVGGIGGNRRTFSQQL----LQGVDHLPHTLDIQ 189

Query: 192 EGGDMTP-EEFGIWAANQLEEKILELGVDTVGAFIAEPIQGAGGVIIPPDSYWPRIKEIL 250
           +        E G   A  LE+ +   G + + A I EP+ G+ GVI+PP  Y  R++EI 
Sbjct: 190 QNAFCKGLPETGAEKAEVLEQLVTLHGAENIAAVIVEPMSGSAGVILPPQGYLKRLREIT 249

Query: 251 AKYDILFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEV 310
            KY IL + DEVI GFGR G+ F S  +G+ PDM+T AK L +G IPMG +++ D + + 
Sbjct: 250 RKYGILLIFDEVITGFGRVGDAFASQRWGVTPDMITTAKALNNGTIPMGAVLIDDAIYDA 309

Query: 311 ---LNEGG-DFNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELND 366
                EG  +  HG+TYSGHPVAAA A+  + I +EE++ E  ++    Y +K +  L  
Sbjct: 310 SMDAPEGAIELYHGYTYSGHPVAAAAAIATLDIYQEEQLFERTKS-LEGYFEKAVHSLKG 368

Query: 367 HPLVGEVRGVGLLGAIEL-VQDKATRARYVGKGVGMICRQFCFDNGLIMRAVGDTMIIAP 425
            P + ++R  GL+  I+    DK    R    G G+   + CF NG ++RA  DT+ ++P
Sbjct: 369 LPNLIDIRNTGLVAGIQFSPSDKGIGKR----GFGIF--ETCFKNGTLVRATADTIALSP 422

Query: 426 PLVITKAEIDELV 438
           PL++ +A+ID++V
Sbjct: 423 PLIVDEAQIDQMV 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: 521
Number of extensions: 22
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