GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Nocardioides daejeonensis MJ31

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_162602315.1 DNK54_RS05345 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>NCBI__GCF_003194585.1:WP_162602315.1
          Length = 462

 Score =  143 bits (361), Expect = 7e-39
 Identities = 94/296 (31%), Positives = 155/296 (52%), Gaps = 7/296 (2%)

Query: 5   VQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI-FAG 63
           V  L  GL   SI  + ++G  MV+G  G+ NFAHG++   G   A  +  +  SI  AG
Sbjct: 167 VNLLATGLVYSSILAMASLGLNMVFGTTGLTNFAHGELMTFGALIAFAIDSLPGSISIAG 226

Query: 64  LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLR--GSFRLAPLITAIGMSITLSNFIQV 121
              +V+  V  +V  L + ++ W  ++  + PLR  G+  +A +I +IG+SI L N  Q 
Sbjct: 227 HDFSVV--VACLVGFLASGIFGWLNDKGLWLPLRRRGTGVIAMMIVSIGLSIFLRNLYQY 284

Query: 122 TQGPRNKPIPPMVS-SVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATE 180
             G +N       + S   FG + V+  QI + +++  +L +   ++  T LG+A RA  
Sbjct: 285 FAGGQNHNYSQYTNISPMTFGPLQVTSLQITVFIVSVTVLVVACLLLQYTRLGKATRAVA 344

Query: 181 QDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVL 240
            +  +AA  G+NV++ I+  +V GAALA ++G +  +  G  ++  G+   +  F A  L
Sbjct: 345 DNPALAASSGINVERVINRVWVFGAALAGLSGALLGVTQGF-NYQVGYKALLMIFAAVCL 403

Query: 241 GGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPE 296
           GG+G++ GA+ G  +IG+   L +       K V    +L  VL+ +P GILGR E
Sbjct: 404 GGLGTVWGAIAGAFVIGIFIELSTLVVPDELKYVGALGVLIVVLMVRPQGILGRRE 459


Lambda     K      H
   0.329    0.143    0.421 

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: 351
Number of extensions: 18
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: 300
Length of database: 462
Length adjustment: 30
Effective length of query: 270
Effective length of database: 432
Effective search space:   116640
Effective search space used:   116640
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: 49 (23.5 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