GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Herbaspirillum autotrophicum IAM 14942

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_050462656.1 AKL27_RS09910 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= TCDB::P21628
         (417 letters)



>NCBI__GCF_001189915.1:WP_050462656.1
          Length = 408

 Score =  497 bits (1280), Expect = e-145
 Identities = 258/418 (61%), Positives = 318/418 (76%), Gaps = 15/418 (3%)

Query: 1   MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWT-IAAAALAMFVWQL 59
           M  +LK A+ +A+L  +++ P+LGLKL+  G ++ +     Q  WT +  A LA+F++QL
Sbjct: 1   MPITLKNAVAAAILTAILTTPLLGLKLQLEGYRVVL-----QAHWTPVLIAVLAVFLFQL 55

Query: 60  FRDRIPLKLGRGVGYKVNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATL 119
           F+  +           +    L      P+ QR+A++ L+ VA VWPFF SRG VD+ TL
Sbjct: 56  FKPALSRTTAN-----IRLPALPKLQ--PTQQRYALMVLLAVALVWPFFGSRGNVDVVTL 108

Query: 120 ILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAAL 179
            LIYV+LG+GLNIVVG AGLLDLGYVGFYAVG YTYALL +Y G  FW  LP+A  M+AL
Sbjct: 109 ALIYVVLGLGLNIVVGFAGLLDLGYVGFYAVGGYTYALLNQYFGLSFWECLPLAAGMSAL 168

Query: 180 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFER 239
           FGFLLGFPVLRLRGDYLAIVTLGFGEIIR+LL N+T +TGGP+G+  IPKPT+FG+   R
Sbjct: 169 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRLLLNNLTSLTGGPDGVSGIPKPTVFGIEMAR 228

Query: 240 RAP-EGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALRED 298
            A  EG  TFH+  G+ Y   + VI LY + LLLVL   FV +RL+RMP+GRAWEALR+D
Sbjct: 229 TASVEGGTTFHDMLGLTYQGGHMVIFLYFLGLLLVLFTYFVTSRLIRMPMGRAWEALRDD 288

Query: 299 EVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLG 358
           E+ACR+LG+NPT +KLSAFT+GA+FAG AGSFFAARQGLV PESFTFIESA+ILAIVVLG
Sbjct: 289 EIACRSLGINPTKIKLSAFTLGAAFAGLAGSFFAARQGLVNPESFTFIESALILAIVVLG 348

Query: 359 GMGSQLGVILAAVVMVLLQEM-RGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLEL 415
           GMGSQLGVILAA+++ +L E+ R F EYRMLIFGL M++MMIWRPQGLLP  RPH+EL
Sbjct: 349 GMGSQLGVILAAILLTILPEVARSFAEYRMLIFGLVMVLMMIWRPQGLLPATRPHVEL 406


Lambda     K      H
   0.330    0.146    0.439 

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: 618
Number of extensions: 35
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: 417
Length of database: 408
Length adjustment: 31
Effective length of query: 386
Effective length of database: 377
Effective search space:   145522
Effective search space used:   145522
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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