GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Lutibaculum baratangense AMV1

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_023434296.1 N177_RS20205 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>NCBI__GCF_000496075.1:WP_023434296.1
          Length = 312

 Score =  410 bits (1055), Expect = e-119
 Identities = 214/313 (68%), Positives = 252/313 (80%), Gaps = 14/313 (4%)

Query: 1   MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60
           MEYFVQQL+NGLTLGSIYGL+AIGYTMVYGIIGMINFAHGDIFM+G F ALI  +    +
Sbjct: 1   MEYFVQQLINGLTLGSIYGLIAIGYTMVYGIIGMINFAHGDIFMVGSFIALIAIIAF-GL 59

Query: 61  FAGLPVAVLLLVM---LVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSN 117
            AG  +AVL+L +   L++AM +TS++ WT+ER+AYRPLRGSFRLAPLITAIGMSI L N
Sbjct: 60  TAGSSLAVLILALILVLLIAMALTSVYGWTVERLAYRPLRGSFRLAPLITAIGMSIVLQN 119

Query: 118 FIQVTQGPRNKPIPPMVSSVYQFGN----------ISVSLKQIIIIVITAVLLTIFWYIV 167
           F+Q+ QG R KP+ P+ S  +              +++S  QI+IIV T VL+T+F  I+
Sbjct: 120 FVQIAQGARVKPLQPLFSGGFTLMELEGPTGAVFRVNLSFAQILIIVTTVVLMTVFTLII 179

Query: 168 NRTALGRAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDG 227
            +T+LGR+QRA EQDRKMAALLGVNVD+TIS+TFVMGAALAAVAG MYL+YYGV  F  G
Sbjct: 180 AKTSLGRSQRACEQDRKMAALLGVNVDRTISLTFVMGAALAAVAGLMYLLYYGVIDFYIG 239

Query: 228 FTPGVKAFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFK 287
           F  GVKAFTAAVLGGIGSLPGA+ GGLLIGLIE+ WSAYF+I YKDVA F+ILA VLIF 
Sbjct: 240 FIAGVKAFTAAVLGGIGSLPGAMLGGLLIGLIETFWSAYFSIEYKDVAAFSILAIVLIFL 299

Query: 288 PTGILGRPEVEKV 300
           P+GILGRPEVEKV
Sbjct: 300 PSGILGRPEVEKV 312


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: 426
Number of extensions: 14
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: 300
Length of database: 312
Length adjustment: 27
Effective length of query: 273
Effective length of database: 285
Effective search space:    77805
Effective search space used:    77805
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 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