GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-C in Marinobacter adhaerens HP15

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 GFF3783 HP15_3725 PTS system, fructose-specific IIBC component

Query= TCDB::Q5V5X5
         (383 letters)



>FitnessBrowser__Marino:GFF3783
          Length = 587

 Score =  273 bits (697), Expect = 1e-77
 Identities = 155/344 (45%), Positives = 213/344 (61%), Gaps = 26/344 (7%)

Query: 26  LMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWFLAQIGVA-GLTIMVPILGG 84
           L+TGVSFM+P V  GG+ +A+++  G     F+  G+    L QIG      +M+P+L G
Sbjct: 252 LLTGVSFMLPMVVAGGLLIALSFVFGIE--AFQEEGTLAAALMQIGGGTAFKLMIPLLAG 309

Query: 85  YIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAGYLGAIVAGLLAGYVA 144
           YIA++IADRPGLAPG +  ++                  GE GAG+LG IVAG LAGYVA
Sbjct: 310 YIAWSIADRPGLAPGMIGGFL-----------------AGELGAGFLGGIVAGFLAGYVA 352

Query: 145 RFF-KNLDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALANEGLTSFLQSMQGGQ 203
           RF  + L +PE I+ + P+L+IP+    V    M++V+G P+A     LT FL+ M    
Sbjct: 353 RFISQKLPMPESIESLKPILIIPLLASLVTGLGMIYVIGEPMAAIMGALTGFLEGMGTTN 412

Query: 204 AIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEI--YAPMAAVMIGGMIPPIGLALSN 261
           AI++G ILG MM FD+GGPVNK AY F  GL++E     APMAA+M  GM+P IG+ +++
Sbjct: 413 AILLGGILGAMMCFDLGGPVNKAAYTFGVGLLSEGSGGSAPMAAIMAAGMVPAIGMGVAS 472

Query: 262 FIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIVAGSAVGGATSMALG 321
           FIA  K+A    + G++  VLGL FI+EGAIP+ A DPLRVIP  + G A+ GA SM   
Sbjct: 473 FIARRKFAEAERQAGRASFVLGLCFISEGAIPFMAKDPLRVIPVCMIGGAITGALSMLFT 532

Query: 322 VTMPAPHGGIFVVLLSN---QPLAFLGSILLGSLVTAVVATVIK 362
           V + APHGG+FV+ + N     L +L +I +GSLV      ++K
Sbjct: 533 VKLMAPHGGLFVLAIPNAVSAVLPYLIAIAVGSLVIGFGYALLK 576


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: 841
Number of extensions: 47
Number of successful extensions: 5
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: 587
Length adjustment: 33
Effective length of query: 350
Effective length of database: 554
Effective search space:   193900
Effective search space used:   193900
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 17 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