GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Trichormus variabilis ATCC 29413

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_011319366.1 AVA_RS13165 ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_000204075.1:WP_011319366.1
          Length = 491

 Score =  139 bits (350), Expect = 1e-37
 Identities = 79/235 (33%), Positives = 131/235 (55%), Gaps = 14/235 (5%)

Query: 6   LKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFELD 65
           L++ ++SKRF    A + + ++++ G+I+G++G NGAGKTT  N+I GLYQPD G   L 
Sbjct: 3   LRLENISKRFNSFIANDNISLSVDAGKIHGILGENGAGKTTLMNIIGGLYQPDAGEIYLQ 62

Query: 66  GKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAARE 125
            +P   ++P++  K GI   +Q+  L  ++TV EN+++G     ++N +    R K  ++
Sbjct: 63  DQPVKITSPNQAIKLGIGMIYQHFMLVPQLTVTENIILG-----RENSWRLNLRQK--QQ 115

Query: 126 EEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGMN 185
           E AA+ +         G+          L  G Q+R+EI + L    +LL LDEP A + 
Sbjct: 116 EIAALSQA-------YGLEIDPTAKVEDLPVGTQQRVEILKVLYRQAKLLILDEPTAVLT 168

Query: 186 ATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADV 240
            TE   L  +L ++ A G TI+ I H ++ ++ LC+ +TVL  GK +A     D+
Sbjct: 169 PTEVESLINILRQLAAAGNTIIFISHKLEEVINLCDTVTVLRRGKVVATTTTKDM 223



 Score = 56.6 bits (135), Expect = 9e-13
 Identities = 55/225 (24%), Positives = 96/225 (42%), Gaps = 29/225 (12%)

Query: 17  GLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFELDGKPYSPSA--- 73
           G+ A++ V   +  G+I G+ G +G G+    + I  L     GT +L+    SP     
Sbjct: 265 GILAVHNVSFQLLAGEILGIAGVDGNGQRELADAIANLRGILNGTIQLNSS--SPQQKIG 322

Query: 74  --PHEVAKAGIARTF---QNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAREEEA 128
             P +  K G+   F   QN+ L     V + +    H   K +V   +  H     +E 
Sbjct: 323 YIPEDRQKMGLVLQFTIAQNLIL----NVFKKIPFCRHFLLKSSV---IKHHAQVAMQEF 375

Query: 129 AIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGMNATE 188
            IR   + +                LS G+Q+++ +AR LA  P L+   +P  G++   
Sbjct: 376 DIRATGEDI------------QVSQLSGGNQQKVVLARELAGKPDLIVAMQPTRGLDVGA 423

Query: 189 KLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIA 233
              +   L+  +  G  IL I  +++ +M + +RI V+  GK +A
Sbjct: 424 TSAVHSRLLTERDRGAAILYISTELEEVMAMSDRIAVIYRGKFVA 468


Lambda     K      H
   0.320    0.138    0.394 

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: 269
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 255
Length of database: 491
Length adjustment: 29
Effective length of query: 226
Effective length of database: 462
Effective search space:   104412
Effective search space used:   104412
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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