GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pseudomonas stutzeri RCH2

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate GFF305 Psest_0306 adenosylmethionine-8-amino-7-oxononanoate transaminase

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



>FitnessBrowser__psRCH2:GFF305
          Length = 467

 Score =  215 bits (548), Expect = 2e-60
 Identities = 136/437 (31%), Positives = 217/437 (49%), Gaps = 14/437 (3%)

Query: 18  HHLAPFSDFKQLKEKGPRI-ITNAKGVYLWDSEGNKILDGMAGLWCVAIGYGRDELADAA 76
           H      D +QL    P I I    GV+L D +G + LD ++  W    G+    +    
Sbjct: 17  HPCTQMKDHEQL----PLIPIRRGDGVWLEDFDGKRYLDAVSSWWVNVFGHANPRINQRI 72

Query: 77  SKQMRELPYYNLFFQTAHPPVLELAKAISDIAPEGMNHVFFTGSGSEGNDTMLRMVRHYW 136
             Q+ +L +  L    +H PV+EL++ +  + P G++ VF+T +GS G +  L+M  HYW
Sbjct: 73  KDQVDQLEHVMLA-GFSHQPVVELSERLVALTPAGLDRVFYTDNGSTGIEVALKMSFHYW 131

Query: 137 AIKGQPNKKVIISRINGYHGSTVAGASLGGMTYMHEQGDLPIPGIVHIPQPYWFGEGGDM 196
              G+  K+  ++  N YHG TVA  S+G +    +     +     +P P  +     +
Sbjct: 132 RNSGRGQKQRFVTLTNSYHGETVAAMSVGDVALFTDTYKPLLLDTFKVPSPDCYLRPDGV 191

Query: 197 TPEEFGIWAANQLEEKILELGVDTVGAFIAEP-IQGAGGVIIPPDSYWPRIKEILAKYDI 255
           + EE        +E+ + E   D + A I EP IQGAGG+ +    Y   ++E   +Y++
Sbjct: 192 SWEEHSRQMFAHMEQTLAEHHQD-IAAVIVEPLIQGAGGMRMYHPVYLKLLREACDRYEV 250

Query: 256 LFVADEVICGFGRTGEWFGSDFYGLKPDMMTIAKGLTSGYIPMGGLIVRDEVVEVLNEGG 315
             + DE+  GFGRTG  F  +  G+ PD + ++K LT GY+PM  ++  D + +   +  
Sbjct: 251 HLIHDEIAVGFGRTGTMFACEQAGITPDFLCLSKALTGGYLPMAAVLTTDRIYQAFYDDY 310

Query: 316 D----FNHGFTYSGHPVAAAVALENIRILREEKIIEHVRAETAPYLQKRLRELNDHPLVG 371
                F H  TY+G+P+A A AL  + I  E+ +IE      A  +      L DHP V 
Sbjct: 311 STLRAFLHSHTYTGNPLACAAALATLDIFAEDNVIE-ANKPLAARMASATAHLVDHPHVA 369

Query: 372 EVRGVGLLGAIELVQDKATRARYV-GKGVGMICRQFCFDNGLIMRAVGDTMIIAPPLVIT 430
           EVR  G+  AIE+VQDKA+R  Y   +  G+   Q   + G ++R +G  +   PP  IT
Sbjct: 370 EVRQTGMALAIEMVQDKASRTAYPWQERRGLKVYQHALERGALLRPLGSVVYFLPPYCIT 429

Query: 431 KAEIDELVTKARKCLDL 447
           + +ID L   A + +D+
Sbjct: 430 EEQIDFLAAVATEGIDI 446


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: 29
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: 467
Length adjustment: 33
Effective length of query: 421
Effective length of database: 434
Effective search space:   182714
Effective search space used:   182714
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