GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00890 in Herbaspirillum autotrophicum IAM 14942

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_050462656.1 AKL27_RS09910 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:D8IUY5
         (404 letters)



>NCBI__GCF_001189915.1:WP_050462656.1
          Length = 408

 Score =  274 bits (700), Expect = 4e-78
 Identities = 166/389 (42%), Positives = 230/389 (59%), Gaps = 61/389 (15%)

Query: 9   KRNPQQARISLLLLLALMIVFPFVAQQFGNSWVRIMDVALLYIMLALGLNVVVGFAGLLD 68
           K  P Q R +L++LLA+ +V+PF   + GN  V ++ +AL+Y++L LGLN+VVGFAGLLD
Sbjct: 74  KLQPTQQRYALMVLLAVALVWPFFGSR-GN--VDVVTLALIYVVLGLGLNIVVGFAGLLD 130

Query: 69  LGYIAFYAIGAYSAGLLASPQFAAVIESFVNTYPSVGNFLVWLCGPEIVQNGIHLSLWLI 128
           LGY+ FYA+G Y+  LL             N Y                     LS W  
Sbjct: 131 LGYVGFYAVGGYTYALL-------------NQY-------------------FGLSFWEC 158

Query: 129 VPISAFLAALFGALLGAPTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGINL 188
           +P++A ++ALFG LLG P L+LRGDYLAIVTLGFGEIIR+ +NNL +   +T GP G++ 
Sbjct: 159 LPLAAGMSALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLLLNNLTS---LTGGPDGVSG 215

Query: 189 IDPIKVFGVSLA---GEPGSGSMVKVFGMSMPS---VNAYYFLFLLLCIGVIFFSVRLQD 242
           I    VFG+ +A      G  +   + G++      V   YFL LLL +   F + RL  
Sbjct: 216 IPKPTVFGIEMARTASVEGGTTFHDMLGLTYQGGHMVIFLYFLGLLLVLFTYFVTSRLIR 275

Query: 243 SRLGRAWVAIREDEIAAKAMGINTRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESFSL 302
             +GRAW A+R+DEIA +++GIN   +KL AF +GA+F G+AG+ F A QG V+PESF+ 
Sbjct: 276 MPMGRAWEALRDDEIACRSLGINPTKIKLSAFTLGAAFAGLAGSFFAARQGLVNPESFTF 335

Query: 303 TESIAVLAMVVLGGIGHIPGVVLGGVILAALPEVLRHVVEPVQMAIFGKVWIDAEVLRQL 362
            ES  +LA+VVLGG+G   GV+L  ++L  LPEV R   E                 R L
Sbjct: 336 IESALILAIVVLGGMGSQLGVILAAILLTILPEVARSFAE----------------YRML 379

Query: 363 LYGLAMVVIMLTRPAGLWPSPR-HEDRPE 390
           ++GL MV++M+ RP GL P+ R H + P+
Sbjct: 380 IFGLVMVLMMIWRPQGLLPATRPHVELPQ 408


Lambda     K      H
   0.327    0.143    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: 426
Number of extensions: 27
Number of successful extensions: 6
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: 404
Length of database: 408
Length adjustment: 31
Effective length of query: 373
Effective length of database: 377
Effective search space:   140621
Effective search space used:   140621
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: 50 (23.9 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