GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Sinorhizobium meliloti 1021

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate SM_b20379 SM_b20379 aminotransferase

Query= BRENDA::Q9I6J2
         (456 letters)



>FitnessBrowser__Smeli:SM_b20379
          Length = 461

 Score =  372 bits (955), Expect = e-107
 Identities = 197/453 (43%), Positives = 280/453 (61%), Gaps = 9/453 (1%)

Query: 7   NAKTREWQALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVN 66
           N +     AL +   + P+T+     E G  +IT  +G+Y+ D EG + ++ +AGL+C  
Sbjct: 2   NDRPNSLHALDKQSLVHPYTNLAVHQETGPHVITGGDGIYVVDDEGKRYIEGLAGLFCAG 61

Query: 67  VGYGREELVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEA 126
           +G+  + LV+AATRQ++ +PFY+ F   +  P + LA+ +  +AP  M+ VFF GSGSEA
Sbjct: 62  LGFSEQRLVEAATRQLKTMPFYHSFAHKSTEPGIRLAEKLLSIAPVPMSKVFFAGSGSEA 121

Query: 127 NDTVLRMVRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHI 186
           NDT ++++ +Y    G+P+KK +I R   YHG TVA  SL G+   H   D PI  I+H 
Sbjct: 122 NDTAIKLIWYYNNALGRPEKKKIISRRKAYHGVTVATASLTGLPFNHRDFDLPIANILHT 181

Query: 187 AQP-YW-YGEGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTY 244
             P YW + E G+ + ++F    A  LE  ILE G E +AAF AEP+  +GGVI PP TY
Sbjct: 182 DCPHYWRFAETGE-TEEDFATRMANNLEAIILEEGPETIAAFFAEPVMVSGGVITPPKTY 240

Query: 245 WPKIREILAKYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVV 304
           + K++ +L KYDIL IADEVICGFGRTG  FGS+ YG  PD++  AK L++ Y+P+  ++
Sbjct: 241 FEKVQAVLRKYDILLIADEVICGFGRTGNMFGSETYGLKPDMISCAKQLSAAYMPISALM 300

Query: 305 VR----DEIVEVLNQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQ 360
           +     D +V+   + G F HGFTY GHPVAAAVALE + I  E  I+  V++  AP  Q
Sbjct: 301 INAKIADALVDQSRKIGTFSHGFTYGGHPVAAAVALEALTIYEEIDIVGHVRS-VAPAFQ 359

Query: 361 KRWQELADHPLVGEARGVGMVAALELVKNKKTRERFTDK-GVGMLCREHCFRNGLIMRAV 419
            R ++L +HPL+GEARGVG+VA LE VK+K TRE F     V     +     G++ R +
Sbjct: 360 DRVRKLGEHPLIGEARGVGLVAGLEFVKDKATRENFPPAWQVANQAGKFATARGVLTRGL 419

Query: 420 GDTMIISPPLVIDPSQIDELITLARKCLDQTAA 452
           GD + + P ++ID  QID+L+T     LD T A
Sbjct: 420 GDMVSLCPAMIIDDEQIDDLMTRMGLALDDTLA 452


Lambda     K      H
   0.320    0.138    0.425 

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: 564
Number of extensions: 25
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: 456
Length of database: 461
Length adjustment: 33
Effective length of query: 423
Effective length of database: 428
Effective search space:   181044
Effective search space used:   181044
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.

Links

Downloads

Related tools

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