GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Desulfatiglans anilini DSM 4660

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_028321170.1 H567_RS0109125 branched-chain amino acid ABC transporter permease

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>NCBI__GCF_000422285.1:WP_028321170.1
          Length = 308

 Score =  270 bits (689), Expect = 4e-77
 Identities = 152/297 (51%), Positives = 204/297 (68%), Gaps = 3/297 (1%)

Query: 7   QLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITWV- 65
           QLINGL++G IY LIA+GYT+VYGI+ MINFAHGEI+M G+F        +   G T   
Sbjct: 13  QLINGLTIGGIYALIALGYTLVYGILFMINFAHGEIFMFGSFAGYAALTFLLQYGFTEQR 72

Query: 66  PLA-LLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGA 124
           PLA +L   +A+M+ +A+ G  +ERIAYRPLR + RLAPLISAIG SIFLQN + I+   
Sbjct: 73  PLASILAAFLAAMVVSALLGTILERIAYRPLRRASRLAPLISAIGASIFLQNVMLIIIKG 132

Query: 125 RSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACEQDK 184
           R + + P L        G  ++S  ++  I+ +  LM G    I RT  GRA RA  +D+
Sbjct: 133 RMQ-VYPDLLHETFFEIGWFNISNFQIMIILGSFFLMAGLYIFIQRTRTGRAMRAVAEDR 191

Query: 185 KMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVLGGI 244
             A L+G++V+R+I +TFV+G+ALAA AG+MV + Y  I+  +GF+ G+KAFTAAVLGGI
Sbjct: 192 SAAALMGIDVNRIIMITFVIGSALAAAAGVMVGMYYTQINHMMGFIPGIKAFTAAVLGGI 251

Query: 245 GSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIEKV 301
           G++PGAMLGG+ +GL EAF   +M +++KDV  F +LVLVLIFRP G+LG    EKV
Sbjct: 252 GNVPGAMLGGLFLGLAEAFGVLFMPAQYKDVIAFALLVLVLIFRPRGILGEVVSEKV 308


Lambda     K      H
   0.329    0.144    0.425 

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: 338
Number of extensions: 18
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: 301
Length of database: 308
Length adjustment: 27
Effective length of query: 274
Effective length of database: 281
Effective search space:    76994
Effective search space used:    76994
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 (21.8 bits)
S2: 48 (23.1 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