Alignments for a candidate for pgmA in Lacinutrix algicola AKS293

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Lacinutrix algicola AKS293

Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_055437630.1 ASC41_RS15750 phospho-sugar mutase

Query= SwissProt::P18159
         (581 letters)



>NCBI__GCF_001418085.1:WP_055437630.1
          Length = 575

 Score =  413 bits (1061), Expect = e-119
 Identities = 223/520 (42%), Positives = 327/520 (62%), Gaps = 17/520 (3%)

Query: 34  LEDCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGFAAYISKQGEEAKKRGVVIAYD 93
           L++ FYKDLEFGTGGMRG +G GTNR+N YT+ K + G + Y+ K       + V IA+D
Sbjct: 38  LKESFYKDLEFGTGGMRGVMGIGTNRINKYTLGKNTQGLSDYMHKVFPNETLK-VAIAFD 96

Query: 94  SRHKSPEFAMEAAKTLATQGIQTYVFDELRPTPELSFAVRQLNAYGGIVVTASHNPPEYN 153
            RH S   A   A   +   I+ ++F++LR TPELSFA++ LN + GIV+TASHNPPEYN
Sbjct: 97  CRHNSKSLAKVVANVFSANNIEVFLFEDLRATPELSFALKHLNCHCGIVLTASHNPPEYN 156

Query: 154 GYKVYGDDGGQLPPKEADIVIEQVNAIEN-ELTITVDEENKLKEKGLIKIIGEDIDKVYT 212
           GYKVY  DGGQL P +   +I  +N ++  E+    +E        LI  IG+++D V+ 
Sbjct: 157 GYKVYWQDGGQLVPPQDGEIINVINNLDYAEIKFEANEN-------LINYIGKEVDDVFI 209

Query: 213 E---KLTSISVHPELSEEVDVKVVFTPLHGTANKPVRRGLEALGYKNVTVVKEQELPDSN 269
               K  S +   E  E++++  VFT LHGT+   V   L   GY NV +V+EQ  P+ +
Sbjct: 210 NASVKNGSFNTSAEAREKLNI--VFTSLHGTSITAVPETLNRAGYTNVNIVEEQREPNGD 267

Query: 270 FSTVTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRLGIAVKNDQGKYTVLTGNQTG 329
           F TV SPNPEE  A + AI+L  + +ADI+I TDPD DRLG+ V++   +  +L GNQ  
Sbjct: 268 FPTVVSPNPEEPEALKMAIELATKTDADIVIGTDPDCDRLGVVVRDLDNELVILNGNQAM 327

Query: 330 ALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSFGLDTIDTLTGFKFIGEKIKE 389
            L+  +LL + + +  +  N  +  TIV++ +   +A S+ +++   LTGFK+I + IK+
Sbjct: 328 LLMTDFLLKQWQSENRINGNQFIASTIVSTPMMSVLAESYNVESKIGLTGFKWIAKMIKD 387

Query: 390 YEASGQYTFQFGYEESYGYLIGDFARDKDAIQAALLAVEVCAFYKKQGMSLYEALINLFN 449
           +    +  F  G EES+G+++GDF RDKDA+ + LLA E+ A  K +  S+Y+ LI L+ 
Sbjct: 388 FP---EQDFIGGGEESFGFMVGDFVRDKDAVTSTLLACEIAAQAKAKSSSVYQELIKLYI 444

Query: 450 EYGFYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAGKQVVTAEDYAVSKRTLLTES 509
           E+G Y+E L S+T KG +GA++I+ ++   R+NP + + G+++V  EDY  S    +   
Sbjct: 445 EHGLYKERLISITKKGIEGAKEIKQMMIDARENPLKNVNGEKIVLIEDYQSSIAKNIQSQ 504

Query: 510 KEEAIDLPKSNVLKYFLEDGSWFCLRPSGTEPKVKFYFAV 549
           +E  +D+PKSNVL Y+ EDGS   LRPSGTEPK+KFY +V
Sbjct: 505 EEYILDVPKSNVLIYYTEDGSKIALRPSGTEPKIKFYISV 544


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: 816
Number of extensions: 32
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.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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 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