GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08260 in Herbaspirillum seropedicae SmR1

Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate HSERO_RS08270 HSERO_RS08270 amino acid ABC transporter substrate-binding protein

Query= uniprot:G8ALJ3
         (366 letters)



>FitnessBrowser__HerbieS:HSERO_RS08270
          Length = 373

 Score =  296 bits (758), Expect = 6e-85
 Identities = 154/355 (43%), Positives = 221/355 (62%), Gaps = 3/355 (0%)

Query: 7   LLVAVAATAMTASVAKAD-IAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQK 65
           + +A A  A  A VA A+ + +A AGP+TG  A +G+ +K G   A+  INAAGG  G K
Sbjct: 10  IALAAATFAAFAGVAHAETVKIAIAGPMTGAVAQYGDMVKAGALTAIEQINAAGGANGNK 69

Query: 66  LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTN 125
            +  + DDAC+PKQAVAVAN++   G+K+V GH CSGS+IPAS +Y  EGV+ I+P++T 
Sbjct: 70  FEAVMMDDACEPKQAVAVANKIVSQGIKYVIGHVCSGSTIPASDIYENEGVVMITPSATA 129

Query: 126 PKLTEQNL-KNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKAL 184
           P+LTE    K +FR  GRDDQQG  A +Y++E  K K VA+LHDK +YG+G+A   + AL
Sbjct: 130 PQLTEAKPHKFIFRTIGRDDQQGPAAARYVIEKLKPKKVAVLHDKQSYGQGVASSVKAAL 189

Query: 185 NAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPI 244
           +A      ++E   AG+ DYSA+V+KLK + VD VY GGYH E GL+ RQ ++QG+ A  
Sbjct: 190 DAAKVPVVVFEGINAGDSDYSAIVTKLKSQGVDFVYFGGYHPEMGLIMRQAREQGIKAVF 249

Query: 245 VSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEG-YTLYTYA 303
           +  + +   +  AI GPA E  ++T   D    P     V+ F  A  +P G + +  Y+
Sbjct: 250 MGPEGVGNKDITAIAGPASEGMLVTLPADFAADPANAALVKAFAAAKRDPNGPFQMPAYS 309

Query: 304 ALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWN 358
            ++I A+A   A STD  K+A  +  NS+ T IG + +D KGD+ S  +V + W+
Sbjct: 310 GVKIIADAIAGAKSTDPEKVAAYIHANSFKTPIGNVEYDKKGDLKSFKFVVFTWH 364


Lambda     K      H
   0.312    0.129    0.366 

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: 411
Number of extensions: 24
Number of successful extensions: 3
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: 366
Length of database: 373
Length adjustment: 30
Effective length of query: 336
Effective length of database: 343
Effective search space:   115248
Effective search space used:   115248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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