Alignments for a candidate for pgmA in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Flavobacterium beibuense F44-8

Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_035130453.1 Q763_RS01705 phospho-sugar mutase

Query= SwissProt::P18159
         (581 letters)



>NCBI__GCF_000769915.1:WP_035130453.1
          Length = 575

 Score =  472 bits (1215), Expect = e-137
 Identities = 257/548 (46%), Positives = 352/548 (64%), Gaps = 19/548 (3%)

Query: 34  LEDCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGFAAYISK--QGEEAKKRGVVIA 91
           LED FYK+LEFGTGGMRG +G GTNR+N YT+ KA+ G + Y+ K   GEE K   V IA
Sbjct: 38  LEDSFYKNLEFGTGGMRGIMGPGTNRINKYTLGKATQGLSNYLKKVFTGEEIK---VAIA 94

Query: 92  YDSRHKSPEFAMEAAKTLATQGIQTYVFDELRPTPELSFAVRQLNAYGGIVVTASHNPPE 151
           YD R+ S   A   A   +  GI+ ++F +LRPTPELSFAVR L+ + GIV+TASHNPPE
Sbjct: 95  YDCRNNSNTLAKVVADVFSANGIKVFLFTDLRPTPELSFAVRYLSCHAGIVLTASHNPPE 154

Query: 152 YNGYKVYGDDGGQLPPKEADIVIEQVNAIE-NELTITVDEENKLKEKGLIKIIGEDIDKV 210
           YNGYKVY  DGGQL P +   +I  + A+E N++    +E        LI+ I  D+DK 
Sbjct: 155 YNGYKVYWQDGGQLVPPQDGEIINIIEALEYNQINFNANEN-------LIEYIDNDVDKA 207

Query: 211 YTEKLTSISVHPELSEEVD-VKVVFTPLHGTANKPVRRGLEALGYKNVTVVKEQELPDSN 269
           +       +      E  D +KVVFTPLHGT+ K +   LE  GY NV +V EQ +PD N
Sbjct: 208 FLGASLGAATFNTPQEAKDALKVVFTPLHGTSVKLIPDLLEDAGYSNVHIVNEQAVPDGN 267

Query: 270 FSTVTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRLGIAVKNDQGKYTVLTGNQTG 329
           F TV SPNPEE  A   AI+L  + NADI++ TDPD+DRLG+AV+N +G  T+L GNQT 
Sbjct: 268 FPTVKSPNPEEPEALAMAIELANQTNADIVVGTDPDSDRLGVAVRNSEGIMTLLNGNQTM 327

Query: 330 ALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSFGLDTIDTLTGFKFIGEKIKE 389
            L+ H+LL E KKQG L  N  +  TIV++ +   +A+ +G+     LTGFK+I + I +
Sbjct: 328 MLMTHFLLEEWKKQGKLTGNQFIGSTIVSTPMLMELATDYGVQCKVGLTGFKWIAKMIVD 387

Query: 390 YEASGQYTFQFGYEESYGYLIGDFARDKDAIQAALLAVEVCAFYKKQGMSLYEALINLFN 449
           +    +  F  G EES+GY++GDF RDKDA+ + LL  E+ A  K    SLY+ L+ L+ 
Sbjct: 388 FP---ELQFIGGGEESFGYMVGDFVRDKDAVTSTLLLCEIAAQAKANASSLYQELLKLYT 444

Query: 450 EYGFYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAGKQVVTAEDYAVSKRTLLTES 509
           +YGFY+E L SLT KG  GA++I+ ++   R++P +++ G++VV  EDY  S    L   
Sbjct: 445 KYGFYKEYLISLTKKGMDGAQEIKQMMIDLRESPLKEINGERVVMVEDYQASTSKNLFTD 504

Query: 510 KEEAIDLPKSNVLKYFLEDGSWFCLRPSGTEPKVKFYFAVKGS--SLEDSEKRLAVLSED 567
           +EEA+ LPKSNVL Y+LEDG+  C RPSGTEPK+KFYF+V  +   +E++ +   +L   
Sbjct: 505 EEEALTLPKSNVLIYYLEDGTKICARPSGTEPKIKFYFSVNDTLDKVENAREVETILDHK 564

Query: 568 VMKTVDEI 575
           +   ++E+
Sbjct: 565 IRNIIEEM 572


Lambda     K      H
   0.313    0.133    0.371 

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: 854
Number of extensions: 34
Number of successful extensions: 4
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: 581
Length of database: 575
Length adjustment: 36
Effective length of query: 545
Effective length of database: 539
Effective search space:   293755
Effective search space used:   293755
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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 2024 update 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