GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2215
          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.

Links

Downloads

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:

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