GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Williamsia sterculiae CPCC 203464

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_076476008.1 BW971_RS02060 4-aminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::Q88RB9
         (425 letters)



>NCBI__GCF_900156495.1:WP_076476008.1
          Length = 452

 Score =  347 bits (889), Expect = e-100
 Identities = 180/424 (42%), Positives = 252/424 (59%), Gaps = 3/424 (0%)

Query: 5   NESLMQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVV 64
           + +L +RR AAV  GVG + PI+   A    ++DV+G  LID   GIAV   G  +P V 
Sbjct: 24  SSALAKRRAAAVAAGVGSVVPIYAADADGGIIVDVDGNSLIDLGSGIAVTGVGASNPAVA 83

Query: 65  AAVQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIAR 124
            AV  Q    +HTCF V  YE YV + EK+N+L PGD +K+++L  +G+EAVENAVK+AR
Sbjct: 84  DAVAAQAHHFTHTCFMVTPYEGYVAVAEKLNELTPGDHEKRSVLFNSGAEAVENAVKVAR 143

Query: 125 AATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGISVDDA 184
            ATGR  ++AF   YHGRT +T+ LT K  PY    G     I+R             D 
Sbjct: 144 LATGRDAIVAFDHAYHGRTNLTMALTAKTQPYKYNFGPFAPEIYRMPMSYPYRDDLGTDG 203

Query: 185 IASVERIFKN---DAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIADE 241
           +++ +R  +          +A +++EP+QGEGGF+      +  L      +G++ IADE
Sbjct: 204 VSAAKRAIRQIETQIGGEAVAGLLIEPIQGEGGFIVPAPGFLTTLAEWARDNGVVFIADE 263

Query: 242 VQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAG 301
           VQ G  RTGT+FA E  G+ PD+ T AK IAGG PL+ + G+A+ +D + PGGLGGTY G
Sbjct: 264 VQAGFCRTGTWFASEAEGIVPDIVTTAKGIAGGMPLSAITGRADLLDKVHPGGLGGTYGG 323

Query: 302 SPIACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEVF 361
           +P+ACAAALA I   EE  L  R+  + E     LR +     +IGDVRG G+M+A+E+ 
Sbjct: 324 NPVACAAALATIAEMEELDLNARAHHIEEIALPRLRTLADDLDVIGDVRGRGAMLAIEIV 383

Query: 362 EKGTHTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECF 421
           E GT TP  A   +V A A E G+++L  GT+GNV+R+L PL  +D  L  G+ ++E+  
Sbjct: 384 EPGTDTPAPALAKKVAAAALEAGVVILVTGTFGNVIRLLPPLVIDDETLVDGIDVLEQSL 443

Query: 422 AEIA 425
             +A
Sbjct: 444 HSVA 447


Lambda     K      H
   0.320    0.138    0.395 

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: 589
Number of extensions: 26
Number of successful extensions: 2
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: 425
Length of database: 452
Length adjustment: 32
Effective length of query: 393
Effective length of database: 420
Effective search space:   165060
Effective search space used:   165060
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 24 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