GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Tatumella morbirosei LMG 23360

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_038018174.1 HA49_RS13070 phosphomannomutase/phosphoglucomutase

Query= BRENDA::Q8PGN7
         (450 letters)



>NCBI__GCF_000757425.2:WP_038018174.1
          Length = 459

 Score =  476 bits (1225), Expect = e-139
 Identities = 237/458 (51%), Positives = 322/458 (70%), Gaps = 10/458 (2%)

Query: 1   MPMTLPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALS 60
           M   L  FKAYDIRG++  EL+ D+A RIG A    L+   VV+G DVRL S  L+ +L+
Sbjct: 1   MSTKLSCFKAYDIRGKLDVELDCDVAYRIGRAYGQFLNPKKVVIGGDVRLTSENLKLSLA 60

Query: 61  AGLRASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISS 120
            GL+ SG DVID+G  GTEEVYF T +L A GG+ VTASHNP+DYNGMKLV+E ++PIS 
Sbjct: 61  RGLQDSGVDVIDLGTTGTEEVYFATSHLNADGGIEVTASHNPLDYNGMKLVKEFSKPISG 120

Query: 121 DTGLFAIRDTVAADTAAPGEPTASEQSRTDKTA---YLEHLLSYVDRSTL-KPLKLVVNA 176
           DTGL  I+  +A + + P    +   +    +    Y+  +L+++D   + +P+KLVVN+
Sbjct: 121 DTGLRDIQ-RLAEENSFPDVVNSQRGTYNQLSTLVQYVSMILNFIDLKNISRPIKLVVNS 179

Query: 177 GNGGAGLIVD-----LLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNG 231
           GNG AG ++D      +   +P  F+++ H PDGNFPNGIPNPLLP+ R  T  AV  + 
Sbjct: 180 GNGAAGHVIDEIEKIFIEKKVPISFIKIHHNPDGNFPNGIPNPLLPDCRQDTTDAVIAHN 239

Query: 232 ADFGIAWDGDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQV 291
           AD GIA+DGDFDRCF FD  G FIEGYY+VGLLA++ L K    K++HDPRL+WNT++ V
Sbjct: 240 ADMGIAFDGDFDRCFLFDECGCFIEGYYIVGLLAESFLEKNVNEKIIHDPRLSWNTIDIV 299

Query: 292 EEAGGIPVLCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQ 351
              GGIPV  K+GHAFIKEKMRSE+AVYGGEMSAHHYFR+F Y DSGMIPWLL+ EL+  
Sbjct: 300 TTCGGIPVESKTGHAFIKEKMRSEDAVYGGEMSAHHYFRDFFYCDSGMIPWLLVVELLCV 359

Query: 352 SGRSLADLVEARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQW 411
              +L+ LV  R+ K+P SGEIN  + +   ++  +  +Y  ++  +D+ DG+S +F  W
Sbjct: 360 KNTTLSSLVNKRIDKYPASGEININLKNPSVAIDYIHSYYKGIAVNIDFLDGLSIEFENW 419

Query: 412 RFNLRSSNTEPLLRLNVETRGDAALLETRTQEISNLLR 449
           RFNLRSSNTEP++RLNVE++G+ +L++ +TQE+ ++L+
Sbjct: 420 RFNLRSSNTEPVVRLNVESKGNKSLMQLKTQELLDILK 457


Lambda     K      H
   0.319    0.136    0.404 

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: 575
Number of extensions: 22
Number of successful extensions: 3
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: 450
Length of database: 459
Length adjustment: 33
Effective length of query: 417
Effective length of database: 426
Effective search space:   177642
Effective search space used:   177642
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: 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