GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Limnohabitans curvus MWH-C5

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_108401790.1 B9Z44_RS04225 branched-chain amino acid ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>NCBI__GCF_003063475.1:WP_108401790.1
          Length = 309

 Score =  255 bits (651), Expect = 1e-72
 Identities = 139/303 (45%), Positives = 202/303 (66%), Gaps = 15/303 (4%)

Query: 8   LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67
           LQQ++NGL +GS YAL+A+GYTMVYGII +INFAHGEV MIG+  ++  I LL  +  D+
Sbjct: 5   LQQVINGLVLGSMYALVALGYTMVYGIINLINFAHGEVLMIGALCSWSVIGLLQPLMPDT 64

Query: 68  VP-LMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD 126
              +++L +   + I  +A  Y+IE++AYRPLR   +L PLI+AIGMSI LQ   M+   
Sbjct: 65  PGWVLLLISMVLASIAAAALNYAIEKIAYRPLRNAPKLAPLITAIGMSILLQTLAMIVWK 124

Query: 127 SKEKAIPTLLPGN-FVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185
              K  PTLLP   F  GE+     VI+  Q++I  +T + +  L+  ++R++LGRA RA
Sbjct: 125 PNYKPFPTLLPTTPFEIGEA-----VITPTQLMILGLTAVALAVLSWLVNRTKLGRAMRA 179

Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245
            AE+ ++ +L+G+  + +I+ TF+IGA LA +A V+  M YG  +  +GFL G+KAFTAA
Sbjct: 180 TAENPRVASLMGVKPDVVISATFIIGAVLATIAGVMWAMNYGTAHHAMGFLPGLKAFTAA 239

Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGA--------DVFGDQYKDVVAFGLLILVLLFRPTG 297
           V GGIG++ GA++GGLLLG+ E+ G+         V G  Y D++AF +LI+ L  RP+G
Sbjct: 240 VFGGIGNLGGAVVGGLLLGLIESIGSGYLGELTGGVLGSHYTDILAFVVLIITLTLRPSG 299

Query: 298 ILG 300
           +LG
Sbjct: 300 LLG 302


Lambda     K      H
   0.328    0.145    0.413 

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: 317
Number of extensions: 16
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: 307
Length of database: 309
Length adjustment: 27
Effective length of query: 280
Effective length of database: 282
Effective search space:    78960
Effective search space used:    78960
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 24 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 (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