GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00870 in Azospirillum thiophilum BV-S

Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate WP_045585058.1 AL072_RS29535 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:D8IUY1
         (378 letters)



>NCBI__GCF_001305595.1:WP_045585058.1
          Length = 366

 Score =  197 bits (500), Expect = 5e-55
 Identities = 123/361 (34%), Positives = 197/361 (54%), Gaps = 8/361 (2%)

Query: 11  IAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITVGGK 70
           + A++A     A A +  +  +  + P+TG  A+ G+  + G+  A+  +NA    V G+
Sbjct: 7   LLAAIAATALSATAAKADIA-VATAGPITGQYATFGEQMKKGMEQAVADINAAG-GVLGQ 64

Query: 71  KIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGIV-VATV 129
           K+K +V   DD  DPK  VAVA +LA  GVK + G + SG +IPAS+VY + G++ ++  
Sbjct: 65  KLKLEV--GDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGMLQISPA 122

Query: 130 ASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQEFIK 189
           ++NPK+T+QG   +FRV   D Q G     Y  ++ K K VA++ D++AYG+GLA E  K
Sbjct: 123 STNPKLTEQGLKNVFRVCGRDDQQGMIAGKYLLEKYKGKNVAILHDKSAYGKGLADETQK 182

Query: 190 VAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLGVDV 249
              A G      +       D++A+++ +K    DAV++GGY  + G + RQMK  G+  
Sbjct: 183 ALNAGGQKEAIYEAYTAGEKDYSALVSKLKQANVDAVYVGGYHTEAGLLARQMKDQGLKA 242

Query: 250 PLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAETYAV 309
           P++ GD + + E   + GDA GE    T G    +KA + K   ++++K    P E Y +
Sbjct: 243 PIVSGDALVTNEYWAITGDA-GEDTMMTFGPDPREKA-DAKAVVEKFRKAGYEP-EGYTL 299

Query: 310 SFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVYRFKD 369
             Y  + + A+A+KQA S D  +    L K SY+ V G+  FDA  D+       Y++ +
Sbjct: 300 YTYAALQIWAEAVKQAKSTDAAKVSEVLRKGSYETVIGKIGFDAKGDVTSPAYVWYKWHN 359

Query: 370 G 370
           G
Sbjct: 360 G 360


Lambda     K      H
   0.316    0.134    0.378 

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: 27
Number of successful extensions: 8
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: 378
Length of database: 366
Length adjustment: 30
Effective length of query: 348
Effective length of database: 336
Effective search space:   116928
Effective search space used:   116928
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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