GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-C in Rhodobacter viridis JA737

Align Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate WP_110805521.1 C8J30_RS09070 PTS fructose-like transporter subunit IIB

Query= TCDB::Q5V5X5
         (383 letters)



>NCBI__GCF_003217355.1:WP_110805521.1
          Length = 578

 Score =  298 bits (762), Expect = 3e-85
 Identities = 163/342 (47%), Positives = 225/342 (65%), Gaps = 24/342 (7%)

Query: 26  LMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWFLAQIGVAGLTIMVPILGGY 85
           L+TGVS+M+P V  GG+ +A+++  G      E T  A   +A  G A   +MVP+L G+
Sbjct: 245 LLTGVSYMLPLVVAGGLLIALSFVFGIKAFEVEGTLPAA-LMAIGGGAAFKLMVPVLAGF 303

Query: 86  IAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAGYLGAIVAGLLAGYVAR 145
           IAY+IADRPGL PG +       G ++A              AG+LG IVAG LAGYVAR
Sbjct: 304 IAYSIADRPGLTPGLI-------GGMLAV----------NLNAGFLGGIVAGFLAGYVAR 346

Query: 146 FFKN-LDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALANEGLTSFLQSMQGGQA 204
           + ++ + +P  ++ + PVL++P+ + A+   +M++++G PVA     +T+FLQ +    A
Sbjct: 347 WLRDAIQLPRTLEGLKPVLILPLLSTAITGLVMVYIVGTPVAALLAAMTAFLQGLGTTNA 406

Query: 205 IVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMAAVMIGGMIPPIGLALSNFIA 264
           +V+GLILGGMMA DMGGP+NK AY FA GL+T   YAPMAAVM  GM PP+GLAL+  +A
Sbjct: 407 VVLGLILGGMMAVDMGGPINKAAYTFAVGLLTSNTYAPMAAVMAAGMTPPLGLALATLVA 466

Query: 265 PHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIVAGSAVGGATSMALGVTM 324
            +++ AE  E G +  VLGLSFITEGAIP+AA DP RVIP+I+ GSA+ GA SMALG  +
Sbjct: 467 KNRFTAEEREAGGAAAVLGLSFITEGAIPFAAKDPARVIPSIIVGSAITGALSMALGCLL 526

Query: 325 PAPHGGIFVVLLSNQPLAFLG----SILLGSLVTAVVATVIK 362
            APHGGIFV+ + N  +  LG    SI++G+LVT  +   +K
Sbjct: 527 VAPHGGIFVLAIPN-AVTNLGLYALSIVVGTLVTTGLLIALK 567


Lambda     K      H
   0.322    0.139    0.399 

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: 767
Number of extensions: 39
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: 383
Length of database: 578
Length adjustment: 33
Effective length of query: 350
Effective length of database: 545
Effective search space:   190750
Effective search space used:   190750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 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