GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Paludibacter propionicigenes WB4

Align Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized)
to candidate WP_013444375.1 PALPR_RS04220 phospho-sugar mutase

Query= SwissProt::Q96G03
         (612 letters)



>NCBI__GCF_000183135.1:WP_013444375.1
          Length = 582

 Score =  323 bits (827), Expect = 2e-92
 Identities = 196/579 (33%), Positives = 314/579 (54%), Gaps = 24/579 (4%)

Query: 22  WLRWDKNSLTLEAVKRLIAEGNKEELRKCFGARMEFGTAGLRAAMGPGISRMNDLTIIQT 81
           WL  + N  T + V+RL+   +K EL + F   +EFGT GLR  MG G +RMN  T+   
Sbjct: 17  WLDGNYNEETKKEVRRLLEAEDKSELIESFYRDLEFGTGGLRGIMGVGTNRMNIYTVGAA 76

Query: 82  TQGFCRYLEKQFSDLKQKGIVISFDARAHPSSGGSSRRFARLAATTFISQGIPVYLFSDI 141
           TQG   YL+ QF D+ Q  +VI  D R       +SR F+ ++A  F + GI VYLF D+
Sbjct: 77  TQGLSNYLKAQFPDVPQLSVVIGHDCR------NNSRLFSEISANIFSANGIKVYLFEDL 130

Query: 142 TPTPFVPFTVSHLKLCAGIMITASHNPKQDNGYKVYWDNGAQIISPHDKGISQAIEENLE 201
            PTP   F + HL   +GI++TASHNPK+ NGYK YW++GAQ+++PHD+ +   + +   
Sbjct: 131 RPTPEASFAIRHLGCQSGIILTASHNPKEYNGYKAYWNDGAQMVAPHDENVITEVNK--- 187

Query: 202 PWPQAWDDSLIDSSP-LLHNPSASINNDYFEDLKKYCFH-RSVNRETKVKFVHTSVHGVG 259
               + DD   + +P L+      I+  + E++KK      S+ R + +K V+T +HG G
Sbjct: 188 --IASVDDIKFEGNPALIEIIGEEIDKLFIENIKKLSLSPESIKRNSNLKIVYTPIHGTG 245

Query: 260 HSFVQSAFKAFDLVPPEAVPEQKDPDPEFPTVKYPNPEEGKGVLTLSFALADKTKARIVL 319
              +  A K +      AVPEQ      FPTV  PNPEE    L ++   A +T A IV+
Sbjct: 246 VKLIPRALKEYGFTNIIAVPEQNVVSGNFPTVVSPNPEE-PAALDMAVKKAIETDADIVM 304

Query: 320 ANDPDADRLAVAEKQDSGEWRVFSGNELGALLGWWLFTSWKEKNQDRSALKDTYMLSSTV 379
           A+DPDADRL +A K D GEW + +GN+   L  ++L   WKE  +      + Y++ + V
Sbjct: 305 ASDPDADRLGIAVKNDKGEWILVNGNQTALLFIYYLIRRWKELGKLNG---NQYIVKTIV 361

Query: 380 SSKILRAIALKEGFHFEETLTGFKWMGNRAKQLIDQG-KTVLFAFEEAIGYMCCPFVLDK 438
           +++I++ IA + G    +  TGFKW+    ++  ++G K  +   EE+ G++   F  DK
Sbjct: 362 TTEIIKQIAERNGVEMFDCFTGFKWIAAVIRE--NEGKKEYIGGGEESYGFLPEEFARDK 419

Query: 439 DGVSAAVISAELASFLATKNLSLSQQLKAIYVEYGYHITKASYFICHDQETIKKLFENLR 498
           D VS+  + AE+A++      +L + L+ IYVEYGY   K    +   +   +++ + +R
Sbjct: 420 DAVSSCTVMAEIAAWAKDNGKTLFELLQDIYVEYGYGKEKGISVVRKGKSGAEEIAQMMR 479

Query: 499 NYDGKNNYPKACGKFEISAIRDL-TTGYDDSQPDKKAVLPTSKSSQMITFTFANGGVATM 557
           ++  ++N PK     ++  ++D  +    D    K + L    +S ++ +   +G   ++
Sbjct: 480 DF--RSNPPKEIAGSKVKVVKDYDSLKMTDLDSGKVSDLIMPATSNVLQYFTEDGTKISV 537

Query: 558 RTSGTEPKIKYYAEL-CAPPGNSDPEQLKKELNELVSAI 595
           R SGTEPKIK+Y E+  A    +D +      N+ + A+
Sbjct: 538 RPSGTEPKIKFYIEVRGAMTSRADYDAADAAANKKIEAV 576


Lambda     K      H
   0.317    0.133    0.399 

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: 891
Number of extensions: 47
Number of successful extensions: 7
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: 612
Length of database: 582
Length adjustment: 37
Effective length of query: 575
Effective length of database: 545
Effective search space:   313375
Effective search space used:   313375
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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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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