GapMind for catabolism of small carbon sources

 

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

Align BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized)
to candidate WP_045585058.1 AL072_RS29535 branched-chain amino acid ABC transporter substrate-binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>NCBI__GCF_001305595.1:WP_045585058.1
          Length = 366

 Score =  395 bits (1014), Expect = e-114
 Identities = 198/357 (55%), Positives = 254/357 (71%), Gaps = 3/357 (0%)

Query: 2   KKSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGI 61
           K SLL+A+A TA+ A +  A AD+ +A AGP+TG  A FG Q++KG EQA ADINAAGG+
Sbjct: 4   KLSLLAAIAATALSATA--AKADIAVATAGPITGQYATFGEQMKKGMEQAVADINAAGGV 61

Query: 62  NGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHP 121
            G+++K+E+GDD  DPKQ ++VAN+ A  GVKFV GHF SG SIPAS+VYAE G+L+  P
Sbjct: 62  LGQKLKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGMLQISP 121

Query: 122 GRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETK 181
               P L   GL N FR CGRDDQQG IAGKYL + +K   +A++HDK+ YG+GLADET+
Sbjct: 122 ASTNPKLTEQGLKNVFRVCGRDDQQGMIAGKYLLEKYKGKNVAILHDKSAYGKGLADETQ 181

Query: 182 KAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLK 241
           KA+NA G  E IYE    G+KD+SAL++K+K+A V  +Y GG HTEAGL+ RQ  DQGLK
Sbjct: 182 KALNAGGQKEAIYEAYTAGEKDYSALVSKLKQANVDAVYVGGYHTEAGLLARQMKDQGLK 241

Query: 242 ATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAYTLYS 301
           A +VSGD +V+NE  +I GDA   T+ TFGPDP      K +VEKF+ AG+ PE YTLY+
Sbjct: 242 APIVSGDALVTNEYWAITGDAGEDTMMTFGPDPREKADAKAVVEKFRKAGYEPEGYTLYT 301

Query: 302 YAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEW 358
           YAA+Q  A A K A S D   V++ ++ KG + TV+G I FD KGD   P Y+ Y+W
Sbjct: 302 YAALQIWAEAVKQAKSTDAAKVSEVLR-KGSYETVIGKIGFDAKGDVTSPAYVWYKW 357


Lambda     K      H
   0.314    0.132    0.383 

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: 469
Number of extensions: 19
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: 381
Length of database: 366
Length adjustment: 30
Effective length of query: 351
Effective length of database: 336
Effective search space:   117936
Effective search space used:   117936
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 (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