GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-C in Caldicellulosiruptor hydrothermalis 108

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_013404311.1 CALHY_RS12545 PTS transporter subunit EIIC

Query= TCDB::Q5V5X5
         (383 letters)



>NCBI__GCF_000166355.1:WP_013404311.1
          Length = 454

 Score =  290 bits (741), Expect = 7e-83
 Identities = 165/359 (45%), Positives = 227/359 (63%), Gaps = 25/359 (6%)

Query: 11  AESALRAHVTSVKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWFLAQI 70
           A+   +   T V + LMTGVS+MIPFV  GGI +A+++A G     FE  G+    L  I
Sbjct: 112 AKKEAKEKATGVYKHLMTGVSYMIPFVVAGGILIAISFAFGIK--AFEKKGTLAAALMDI 169

Query: 71  GV-AGLTIMVPILGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAG 129
           G  +   +MVPIL G+IA++IADRPGL PG                  + G+   + GAG
Sbjct: 170 GGGSAFYLMVPILAGFIAFSIADRPGLVPGM-----------------IGGLLANKLGAG 212

Query: 130 YLGAIVAGLLAGY-VARFFKNLDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALA 188
           +LG IVAG  AGY VA   K + +P+ ++ +MPVL++PV +  ++   M++V+G PVA  
Sbjct: 213 FLGGIVAGFAAGYLVAWLKKTIKLPKTMEGLMPVLILPVLSTLIIGLGMIYVVGEPVAAL 272

Query: 189 NEGLTSFLQSMQGGQAIVVGLILGGMMAFDMGGPVNKVAYVFATG-LITEEIYAPMAAVM 247
           N+ +T +L+SM  G A+++G+ILG MMAFDMGGPVNK AY FA   L   +    MAAVM
Sbjct: 273 NKAMTEWLKSMSSGSAVLLGIILGLMMAFDMGGPVNKAAYTFAVSTLAAGQPSTIMAAVM 332

Query: 248 IGGMIPPIGLALSNFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIV 307
             GM PP+GLAL+  IA  K+  E  E GK+   LG+SFITEGAIP+AAADPLRVIP+I+
Sbjct: 333 AAGMTPPLGLALATLIAKDKFTTEEREAGKAAFFLGISFITEGAIPFAAADPLRVIPSIM 392

Query: 308 AGSAVGGATSMALGVTMPAPHGGIFVVLLSN---QPLAFLGSILLGSLVTAVVATVIKP 363
            GSAV    S+    T+  PHGGIFV+ + N     L +  +I +G++VTA++ +V+KP
Sbjct: 393 IGSAVTSTLSILFKCTLAVPHGGIFVLPIPNAVGNLLLYAVAIAIGTVVTALIVSVLKP 451


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: 621
Number of extensions: 45
Number of successful extensions: 7
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: 454
Length adjustment: 31
Effective length of query: 352
Effective length of database: 423
Effective search space:   148896
Effective search space used:   148896
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: 50 (23.9 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