GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00890 in Dechlorosoma suillum PS

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Dsui_2059 Dsui_2059 ABC-type branched-chain amino acid transport system, permease component

Query= uniprot:A0A165KER0
         (358 letters)



>lcl|FitnessBrowser__PS:Dsui_2059 Dsui_2059 ABC-type branched-chain
           amino acid transport system, permease component
          Length = 287

 Score =  153 bits (386), Expect = 6e-42
 Identities = 108/329 (32%), Positives = 166/329 (50%), Gaps = 60/329 (18%)

Query: 22  LQSFGNAWVRIADLAL---LYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPH 78
           ++ F + W   + L     ++ LLAL + + +   GLL L   AF  VGAY+ AL+   H
Sbjct: 1   MEWFNDFWSTYSTLVFSVGVHALLALSIWLTLS-CGLLSLANAAFMGVGAYVSALLTL-H 58

Query: 79  LADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEI 138
           L  +F +               V+    +       ++GAP L+L G YLA+ TL FGE+
Sbjct: 59  LEWSFGS---------------VLLAGGIAPTLVALIIGAPVLRLSGVYLAMATLAFGEV 103

Query: 139 IRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVV 198
           +RI + NL+    +T GP+GL  I             L   G+ I           +++ 
Sbjct: 104 VRITVLNLE----ITGGPEGLNGIP------------LATEGWHI----------ALILA 137

Query: 199 VSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAF 258
           V+V    RL+ S++GRA+ AI+EDE+AA+ MGIN    KLLAF +GA   GV+GA+   F
Sbjct: 138 VAVYGLARLRRSKVGRAFEAIKEDEVAARLMGINVDRYKLLAFSLGAFIAGVAGALNAHF 197

Query: 259 QGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGR 318
             F+SP  +    +V I+ M VLGG   + G +LG+ +L+ LPE+LR +           
Sbjct: 198 TFFISPREYGFENAVDILTMAVLGGTSSLIGPMLGSSILTLLPELLRSLQD--------- 248

Query: 319 LDSAILRQLLIALAMIIIMLLRPRGLWPS 347
                 R L+    +++++L  P+GLW S
Sbjct: 249 -----FRSLVNGAVLVLVVLFLPKGLWES 272


Lambda     K      H
   0.328    0.144    0.430 

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: 246
Number of extensions: 13
Number of successful extensions: 4
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: 358
Length of database: 287
Length adjustment: 28
Effective length of query: 330
Effective length of database: 259
Effective search space:    85470
Effective search space used:    85470
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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