GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG in Alkalihalobacterium alkalinitrilicum DSM 22532

Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate WP_078430180.1 BK574_RS22665 glucose-specific PTS transporter subunit IIBC

Query= BRENDA::P69786
         (477 letters)



>NCBI__GCF_002019605.1:WP_078430180.1
          Length = 656

 Score =  478 bits (1229), Expect = e-139
 Identities = 250/481 (51%), Positives = 331/481 (68%), Gaps = 15/481 (3%)

Query: 1   MFKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMP 60
           MFK AF  LQ+VG++LM PVSVLP AG+LLG+G  N   +P     +MAEAGG +F N+ 
Sbjct: 1   MFKKAFGTLQRVGRALMTPVSVLPAAGLLLGLGHENVLDIP-----IMAEAGGVIFGNLA 55

Query: 61  LIFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLA--DTGV 118
           L+FA+GVA+G  + DGV+ LAAV+ Y +M  T+ ++A    +  AE +    +    TGV
Sbjct: 56  LLFAVGVAIGLADGDGVAGLAAVIGYLVMNTTLGIMAG---YYGAETVTVLGIETLQTGV 112

Query: 119 LGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSA 178
            GGII G +AA ++ RFY I+LP +LGFFAGKRFVPII+   A+  G++  F+WPPI   
Sbjct: 113 FGGIIMGLVAAALYKRFYNIELPPFLGFFAGKRFVPIITAATAVLLGIIFVFVWPPIQGV 172

Query: 179 IQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIP 238
           I  FS  A      VA  ++GF +R L+PFGLHHI+  PF  + G +TNAAG V  GD+ 
Sbjct: 173 IDWFSHLATETGTTVAAFVFGFTQRALIPFGLHHIFYQPFWFEFGTFTNAAGDVVRGDMT 232

Query: 239 RYMAGDPTAGK-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGIT 297
           R+ AGDPTAG  ++G F F ++GLPAAA+AI+H A+PE +  V GIM SAALTSFLTGIT
Sbjct: 233 RFFAGDPTAGTFMAGLFPFMLFGLPAAALAIYHEARPERKKAVAGIMASAALTSFLTGIT 292

Query: 298 EPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLF 357
           EPIEF+F+FVAP+L++IH I AG +F I  LLG++ G +FS G ID+++  G S+  WL 
Sbjct: 293 EPIEFAFLFVAPVLFLIHCIFAGFSFVIMDLLGVKAGFTFSGGFIDYVLYWGLSTNSWLI 352

Query: 358 PIVGIGYAIVYYTIFRVLIKALDLKTPGR----EDATEDAKATGTSEMAPALVAAFGGKE 413
             VGI +  VYY  FR  I+  +LKTPGR    E  +E+    G  E+A  ++ A GGK+
Sbjct: 353 IPVGIAFGFVYYFGFRFAIRKWNLKTPGREPKEEQVSEEVAKGGKRELASNVLHALGGKQ 412

Query: 414 NITNLDACITRLRVSVADVSKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEY 473
           NIT LDACITRLRVSV + S+VD A LKKLGA+GV+  G+ +QAIFGT+SD LK ++ + 
Sbjct: 413 NITALDACITRLRVSVKEPSEVDSAQLKKLGASGVLEMGNNIQAIFGTQSDALKGQIKDL 472

Query: 474 I 474
           I
Sbjct: 473 I 473


Lambda     K      H
   0.325    0.140    0.422 

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: 949
Number of extensions: 51
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: 477
Length of database: 656
Length adjustment: 36
Effective length of query: 441
Effective length of database: 620
Effective search space:   273420
Effective search space used:   273420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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