GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Thermoactinomyces daqus H-18

Align Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 (characterized)
to candidate WP_033101249.1 JG50_RS0111465 phospho-sugar mutase

Query= SwissProt::O74478
         (587 letters)



>NCBI__GCF_000763315.1:WP_033101249.1
          Length = 565

 Score =  253 bits (647), Expect = 1e-71
 Identities = 189/572 (33%), Positives = 284/572 (49%), Gaps = 47/572 (8%)

Query: 18  DETTRNEVSQLIKAEDYATLKQIMHPRIGFGTSGLRAEIGAGFARMNCLTVIQASQGFAE 77
           DE T+ E+S L    D   ++   +  + FGT G+R  IGAG  R+N  T+ + + G A 
Sbjct: 17  DEKTKLELSMLT---DEKEIEDRFYQDLKFGTGGVRGLIGAGTNRINLYTIRKITCGLAN 73

Query: 78  YLLQTVPSAAKL-GVVIGHDHRHKSNTFARLTAAVFLQKGFKTYFFDHLVHTPLVPFAVK 136
           YL       AK  GV I  D R  S+ FA+  A V    G K + FD L+ TP++ F VK
Sbjct: 74  YLQAEFGEQAKRQGVAIAFDSRLNSSAFAKEAALVLCATGIKVFLFDRLMPTPVLSFTVK 133

Query: 137 TLGTAAGVMITASHNPAAYNGYKVYWGNGCAIIPPHDKGIAACIEKNLTPITWDKNLVEN 196
            LG  AG++ITASHNP  YNGYKVY   GC ++P +   I   ++  +T +T  K  V N
Sbjct: 134 HLGCIAGIVITASHNPKDYNGYKVYDNKGCQLVPRYTDRITRYVDA-VTDLT--KISVAN 190

Query: 197 HKLADRDFAVGLLKNYWSQLHEFHSEN-------NFSLEMKSLKFVYTPIHGVGLPFVTS 249
           ++ A    A G+LK   +++ +   +        + +    +LK VYTP+HG G   V S
Sbjct: 191 YEQA---MAEGMLKIIGTEVLDAFIDEVLMQTCFDDADAKAALKIVYTPLHGTGNLPVRS 247

Query: 250 ALHLFGEQGDMISVPLQDSPNPDFPTVKFPNPEEEGALDLAYEQADANGISYVLATDPDA 309
            L   G  G  + V  Q+ P+  F TV  PNPE+  AL+L  EQA A G   VL TDPD 
Sbjct: 248 VLERDGFTGVSV-VKAQEFPDSSFSTVSSPNPEDRSALELGIEQAIAGGDDIVLGTDPDC 306

Query: 310 DRFAFAEKINGAWRRFTGDEVGCILAYFIFQEYKNVGKPIDDFYVLSTTVSSAMVKSMAK 369
           DR   A +    +   TG+++G +L +F+  + K+     +   ++ T V+  +   +A+
Sbjct: 307 DRVGVAVRSGEGFTLLTGNQIGALLVHFVLSQRKHALN--EKSTLVKTIVTDELGAKIAQ 364

Query: 370 VEGFHHVETLTGFKWLGNKALELEKQGK---FIGLAYEEALGYMVGSIVRDKDGVNALIT 426
             G + V+TLTGFK++G++    E+ G+   FIG  YEE+ G++VG   RDKD + A + 
Sbjct: 365 SYGLNIVDTLTGFKYIGDQITLYEQTGEKEFFIG--YEESYGFLVGMHARDKDAIVASML 422

Query: 427 FLHLLKRLQLQNLSITEVFEQMSKKYGYYTTQNSYFLSR---DTPKLRALVDALRHYDTK 483
              +    + Q  ++  V   + + YGYY      F         ++++++  LR+  T 
Sbjct: 423 ICEMAAYYKTQGKTLLNVLSDIYEHYGYYFNAIDSFEFNGKVGVEEMQSMMTTLRNKGT- 481

Query: 484 SGYPATLGSKKITNVRDLTTGYDSSSTDGKATLPVSKSSDNVTFELENGEVIMTIRTSGT 543
                TL    I  +RD +TG D         LP S    NV   + N    + IR SGT
Sbjct: 482 -----TL-ITGIIEIRDYSTGIDG--------LPKS----NVLKYILNDGSWIAIRPSGT 523

Query: 544 EPKLKFYICARGHSLEDSIKNATEVKQAIKSE 575
           EPK+K Y          + K    ++  I+ E
Sbjct: 524 EPKIKVYYSVYQPDAYSAQKRLEMIQTTIRKE 555


Lambda     K      H
   0.318    0.135    0.401 

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: 753
Number of extensions: 41
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: 587
Length of database: 565
Length adjustment: 36
Effective length of query: 551
Effective length of database: 529
Effective search space:   291479
Effective search space used:   291479
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