GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Halioglobus japonicus S1-36

Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate WP_084198647.1 C0029_RS18740 aspartate aminotransferase family protein

Query= BRENDA::P9WQ77
         (449 letters)



>NCBI__GCF_002869505.1:WP_084198647.1
          Length = 387

 Score =  137 bits (345), Expect = 6e-37
 Identities = 127/395 (32%), Positives = 173/395 (43%), Gaps = 47/395 (11%)

Query: 44  GSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVA- 102
           G YL D   GRRYLD  + +A + LG N P +       A +   A      S++Y V  
Sbjct: 20  GVYLFDT-EGRRYLDGISGIAVNGLGHNHPGVT------AAIQDQAGKLVHTSNLYGVGP 72

Query: 103 MARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLH 162
                E    + G   +   FF   GA A E A+K A          H  D    T ++ 
Sbjct: 73  QEALAERLTEISG---MERCFFGNSGAEANEAAIKIA------RLHGHNRDVEKPT-IIV 122

Query: 163 LRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQAR 222
           L GAFHGR+  TLS T  +  I A F       + AP              + EA+RQ  
Sbjct: 123 LEGAFHGRTLATLSATGNRQ-IQAGFEPLVSGFVRAPRN------------DLEAIRQIA 169

Query: 223 AAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGT 282
           A       D+  F+AEPIQGEGG      ++   +RE+CD    L++ DEVQTG G TGT
Sbjct: 170 A----NNPDVVAFLAEPIQGEGGVNPLDEDYLRGVREICDAQGWLMMLDEVQTGNGRTGT 225

Query: 283 AWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVRAR 342
            +AYQ +   PD+V   K       +        A N F  P    ST+GGN      A 
Sbjct: 226 WFAYQGMGFIPDVVTTAKGLGNGVPIGACLARGEAANTFG-PGHHGSTYGGNPLVCAAAL 284

Query: 343 RILEVIEAEGLFERAVQHGKYLRARLDELAADFPAV--VLDPRGRGLMCAFSLPTTADRD 400
            ++E +  E +     +    +R   D ++AD  A   + D RGRGLM  F L    DRD
Sbjct: 285 AVVEAVNGEDILTNVERMSALIR---DTISADPAAAPRIKDIRGRGLMLGFQL----DRD 337

Query: 401 --ELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAE 433
             EL++      +++     +TVR  PPL +S  E
Sbjct: 338 CPELVKAALDAGLLINVTAGNTVRLLPPLIISEDE 372


Lambda     K      H
   0.323    0.137    0.412 

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: 405
Number of extensions: 29
Number of successful extensions: 6
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: 449
Length of database: 387
Length adjustment: 31
Effective length of query: 418
Effective length of database: 356
Effective search space:   148808
Effective search space used:   148808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 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