Aligments for a candidate for pgmA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for pgmA in Acidovorax sp. GW101-3H11

Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate Ac3H11_2215 Phosphomannomutase (EC 5.4.2.8)

Query= BRENDA::P26276
         (463 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2215 Phosphomannomutase
           (EC 5.4.2.8)
          Length = 462

 Score =  509 bits (1310), Expect = e-149
 Identities = 258/439 (58%), Positives = 324/439 (73%), Gaps = 8/439 (1%)

Query: 12  SIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQG 71
           +IF+AYDIRG+V  TL  E A  +GRA G+ + A G+  VAVGRDGRLSGP +   LIQG
Sbjct: 6   AIFKAYDIRGIVPSTLNEEVALGLGRAFGTAARAEGQTTVAVGRDGRLSGPAMSAALIQG 65

Query: 72  LVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLANEQI 131
           LV+ G +V DVG+V TP+LY+AA+ L   SG+ +TGSHNP DYNGFK+V+ G  +  E+I
Sbjct: 66  LVEAGIEVIDVGLVTTPLLYFAASTL-CNSGIQVTGSHNPKDYNGFKMVLNGRAIYGEEI 124

Query: 132 QALRERIEKND--LASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVIAP 189
           Q LR  +E+    LA G GSV  VD+LP Y ++I  D+ +A+PMK+VVDCGNG+AG  AP
Sbjct: 125 QGLRRTMEQESWQLAPG-GSVRHVDVLPTYRERIVGDVKLARPMKIVVDCGNGIAGASAP 183

Query: 190 QLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRVG 249
            +  ALGC VI L+ EVDGNFPNHHPDP KPENL+DLI  +KA +A+LGLAFDGDGDR+G
Sbjct: 184 AIFRALGCEVIELFSEVDGNFPNHHPDPSKPENLRDLIDALKASDAELGLAFDGDGDRLG 243

Query: 250 VVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGHS 309
           +VT  GT I+PDR +MLFA+DV+SR PG +IIFDVKCT+RL   I+  GG PVM+KTGHS
Sbjct: 244 IVTKDGTNIFPDRQMMLFAQDVLSRVPGGEIIFDVKCTQRLAPAIAAAGGVPVMFKTGHS 303

Query: 310 LIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFPS 369
           LIK +MKET + L GEMSGH+FFKERW+GFDDG Y+  RLLEILS+ Q D   V +A P+
Sbjct: 304 LIKARMKETNSPLGGEMSGHIFFKERWYGFDDGTYAGCRLLEILSKSQ-DPSAVLNALPT 362

Query: 370 DISTPEINITVTEDSKF---AIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTT 426
             STPE+N+   E       A ++AL          ++T+DG+RVD+P G+GL+RASNTT
Sbjct: 363 SFSTPELNVACAEGEPHRLTAELQALAAGQFAAPATVSTIDGLRVDWPDGFGLIRASNTT 422

Query: 427 PVLVLRFEADTEEELERIK 445
           PVLVLRFE  T E L RI+
Sbjct: 423 PVLVLRFEGHTPEALARIE 441


Lambda     K      H
   0.319    0.138    0.410 

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: 630
Number of extensions: 23
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: 463
Length of database: 462
Length adjustment: 33
Effective length of query: 430
Effective length of database: 429
Effective search space:   184470
Effective search space used:   184470
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 17 2021. The underlying query database was built on Sep 17 2021.

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

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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, or view the source code.

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