Alignments for a candidate for manP in Belnapia rosea CPCC 100156

GapMind for catabolism of small carbon sources

Alignments for a candidate for manP in Belnapia rosea CPCC 100156

Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate WP_090662798.1 BLR02_RS10220 PTS fructose transporter subunit EIIBC

Query= BRENDA::O31645
         (650 letters)



>NCBI__GCF_900101615.1:WP_090662798.1
          Length = 566

 Score =  382 bits (980), Expect = e-110
 Identities = 214/470 (45%), Positives = 300/470 (63%), Gaps = 21/470 (4%)

Query: 2   KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61
           +++AITSCP GIAHT+MAAE L+ AA  LG  I+VETQG +G +N LT EEI  AD ++I
Sbjct: 108 RIVAITSCPTGIAHTFMAAEGLEGAAKALGHQIRVETQGSVGAQNALTPEEIAAADLVLI 167

Query: 62  AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKAL-NGDIPVYRSATKSESGNHQEKKQ 120
           AAD  V+  RF  K++   G +  I   + L+ +AL          AT S +    ++  
Sbjct: 168 AADTQVDLSRFGAKRVFLSGTKAAINDGQALVTRALAEATEQGGAQATASAAPAAGKRSL 227

Query: 121 NPIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIE----QIGS 176
           +  Y+HLM GVSFM+PF V GGLLIA+A  LGG      +   DD+   T+     QIG 
Sbjct: 228 SGPYKHLMTGVSFMLPFTVAGGLLIALAFALGG------IYAFDDAHRDTLAGALFQIGG 281

Query: 177 -ASFSFMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAG 235
            A+ + M+P L GYIAYSIAD+PG+ PGMIGG IAA          AGFLGGI+AGF+AG
Sbjct: 282 KAALALMVPALGGYIAYSIADRPGIAPGMIGGMIAAQ-------LNAGFLGGIVAGFVAG 334

Query: 236 YAALWIKK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMK 294
           Y+  W+ + L++P+ ++ + P++I+PV  +LI GLA +++ G PVA   A LT +L GM+
Sbjct: 335 YSVTWLNRALRLPRTLEGLKPVLILPVLGALITGLALIYVAGGPVAVALAWLTEFLRGMQ 394

Query: 295 GSSSILLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIA 354
           GS +ILL L+LG M++FDMGGPVNK A+ F + ++    Y  M    VA  +PP+GL +A
Sbjct: 395 GSGAILLGLLLGGMMAFDMGGPVNKAAYAFSTGLLASQVYSPMAAAMVAGMVPPLGLALA 454

Query: 355 TFLGKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIG 414
            FL + +F   +RE   AA  +GL  I+EGAIPFAA+DPLRVIP+++AGS     I+M  
Sbjct: 455 AFLFRDRFTPEEREAAPAAGVLGLAFISEGAIPFAAKDPLRVIPALVAGSAVAGAISMAV 514

Query: 415 NVGDRVAHGGP-IVAVLGAVDHVLMFFIAVIAGSLVTALFVNVLKKDITA 463
               RV HGG  ++ +  AV  +  + +A++AG++VTAL + +LK+   A
Sbjct: 515 GAELRVPHGGVFVLPIPNAVSQLGGYVVALLAGTVVTALALRLLKRPAVA 564


Lambda     K      H
   0.319    0.137    0.386 

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: 856
Number of extensions: 50
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: 650
Length of database: 566
Length adjustment: 37
Effective length of query: 613
Effective length of database: 529
Effective search space:   324277
Effective search space used:   324277
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 (21.7 bits)
S2: 53 (25.0 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources