GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Herbaspirillum seropedicae SmR1

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate HSERO_RS17580 HSERO_RS17580 hypothetical protein

Query= SwissProt::Q94AL9
         (477 letters)



>FitnessBrowser__HerbieS:HSERO_RS17580
          Length = 440

 Score =  178 bits (452), Expect = 3e-49
 Identities = 132/418 (31%), Positives = 200/418 (47%), Gaps = 34/418 (8%)

Query: 84  VDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNHAIAD 143
           V G+   L D+ G+RY+DA  G AV   GH HP V+E +  Q+  L +    +   A A+
Sbjct: 17  VAGEGMELIDQDGKRYIDASGGAAVSCLGHGHPRVIEAIRKQVGELAYAHTSFFTTAPAE 76

Query: 144 -FSEALASKLPGDLKVVFFTNSGTEANELALMMAKLY------TGCQDIVAVRNGYHGNA 196
             +  LA   PG L  V+F + G+EA E AL +A+ Y         + I+A R  YHGN 
Sbjct: 77  ELAAMLADAAPGSLNHVYFLSGGSEAVEAALKLARQYYVEVGQPQRRHIIARRQSYHGNT 136

Query: 197 AATMGATGQSMWK---FNVVQNSVHHALNPDPYRGVFGSDGE-------KYAKDLQDLIQ 246
              + A G + W+   F  +    HH      YR    +DGE       + A +L+  I 
Sbjct: 137 LGAL-AIGGNAWRREMFMPMLIEAHHVSPCYAYRN--RADGESDVQYVQRLADELEQKIL 193

Query: 247 YGTTGHIAGFICEAIQGV-GGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFW 305
                 +  F+ E + G   G V     Y         K G L I DEV SG  RTG  +
Sbjct: 194 SLGADQVIAFVAETVVGATAGAVPPVGDYFRKIRAVCDKYGVLLILDEVMSGMGRTGYLF 253

Query: 306 GFEAHNVVPDIVTMAKGIGNGF-PLGAVVTTPEIAGVLTRRSYF----NTFGGNSVSTTA 360
             E   VVPDIV +AKG+G G+ P+GA++ +  I   + R S F    +T+ G++ +  A
Sbjct: 254 ACEEDGVVPDIVVIAKGLGAGYQPIGAMICSDHIYDAVLRGSGFFQHGHTYIGHATACAA 313

Query: 361 GLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKT 420
            +AV   I++E+L EN    G  L+ +L Q       +GD+RGRGL +GVELV++R  K 
Sbjct: 314 AVAVQKTIQEERLLENVRQRGEQLRSELRQAFGDQAHVGDIRGRGLFVGVELVAERSSKL 373

Query: 421 PATAET---LHIMDQMKELGVLIGK-----GGYFGNVFRITPPLCFTKDDADFLVEAM 470
           P + +      +  +  + G+L+        G  G+   + PP   + +D   +V+ +
Sbjct: 374 PLSPDLRTHARVKAEAMKRGLLVYPMGGTIDGKNGDHILLAPPFIASSNDISEIVQRL 431


Lambda     K      H
   0.320    0.136    0.403 

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: 504
Number of extensions: 26
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: 477
Length of database: 440
Length adjustment: 33
Effective length of query: 444
Effective length of database: 407
Effective search space:   180708
Effective search space used:   180708
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 Aug 03 2021. The underlying query database was built on Aug 03 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