GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Sinorhizobium meliloti 1021

Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate SM_b21186 SM_b21186 4-aminobutyrate aminotransferase

Query= SwissProt::Q8ZPV2
         (408 letters)



>FitnessBrowser__Smeli:SM_b21186
          Length = 422

 Score =  231 bits (588), Expect = 4e-65
 Identities = 149/395 (37%), Positives = 209/395 (52%), Gaps = 39/395 (9%)

Query: 27  RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTN-EPALR 85
           R E + +WD++G  YIDFA GIAV   GH HP +  A+  Q +RF H  +     E  + 
Sbjct: 26  RAENAEIWDKEGNRYIDFAAGIAVVNTGHRHPKVIAAVKAQLDRFTHTCHQVVPYENYVH 85

Query: 86  LAKKL---IDATFAERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAFHGRT 142
           LA++L   +   FA++  F  +GAEA E A+K+AR          +  +VAF   FHGRT
Sbjct: 86  LAERLNAIVPGDFAKKTIFVTTGAEAVENAVKIAR------AATGRQAVVAFGGGFHGRT 139

Query: 143 LFTVSAGGQPT-YSQDFAPLPPDIRHAAYN-DLN------SASAL-------IDD-NTCA 186
              ++  G+   Y   F  +P D+ HA +  +L+      S SAL       +D     A
Sbjct: 140 FMGMALTGKVVPYKVGFGAMPADVFHAPFPIELHGVTVEQSLSALKKLFAADVDPARVAA 199

Query: 187 VIVEPVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYAYMHYGVTPD 246
           +I+EPVQGEGG  P   AF++ LRE+CD+H  LLI DEVQTG  RTG+L+A  H+GV PD
Sbjct: 200 IIIEPVQGEGGFYPVPTAFMKALREVCDQHGILLIADEVQTGFARTGKLFAMEHHGVAPD 259

Query: 247 ILTTAKALGGGFPIGAMLTTQDYASVMTPGTHGTTYGGNPLATAVAGKVLDIINTPEMQN 306
           + T AK+L GGFP+ A+    +      PG  G TYGGNPL  A A  VLD+I    +  
Sbjct: 260 LTTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLGGTYGGNPLGIAAAHAVLDVIAEENLCE 319

Query: 307 GVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGC--------VLQTEFAGKAKLIAQEA 358
              Q  +   +RL  +  +     +IRG G +           +   EFA K +L+A E 
Sbjct: 320 RANQLGNRLKQRLAAIREKAPEIVDIRGPGFMNAVEFNDVRTNLPSAEFANKVRLLALE- 378

Query: 359 AKAGVMVLIAG--GDVVRFAPALNVSDEEIATGLD 391
              G+++L  G  G+V+RF   + + DE  A  LD
Sbjct: 379 --KGLILLTCGVHGNVIRFLAPITIQDEVFAEALD 411


Lambda     K      H
   0.320    0.137    0.413 

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: 494
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: 408
Length of database: 422
Length adjustment: 31
Effective length of query: 377
Effective length of database: 391
Effective search space:   147407
Effective search space used:   147407
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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