GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-ABC in Dietzia timorensis ID05-A0528

Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate WP_067471936.1 BJL86_RS06275 PTS transporter subunit EIIA

Query= TCDB::Q0S1N2
         (700 letters)



>NCBI__GCF_001659785.1:WP_067471936.1
          Length = 726

 Score =  678 bits (1749), Expect = 0.0
 Identities = 369/698 (52%), Positives = 467/698 (66%), Gaps = 33/698 (4%)

Query: 14  IISEDLISLDTDLGASKEDVISALSRRLADAGRATEADALRDAALARESQSATGLPGGIA 73
           +I    + LD DLG +KE V+  L+    D GRA + D   +A LARE ++ATG+ GG A
Sbjct: 6   LIETGTVRLDADLGDNKEGVLRTLAGAFVDTGRANDLDGAVEALLAREEKAATGMKGGFA 65

Query: 74  IPHCRSEAVVAASLGFARLAPKVDFGAPDGPADLVFLIAAPEGAGAEHMKLLSSLARALV 133
           IPHC+S A+   SL FARL+  VDFGA DGPADLVF++ AP+G G  H+K+LS LAR+LV
Sbjct: 66  IPHCKSAAIDTPSLAFARLSNPVDFGAADGPADLVFMLGAPDGEGKAHLKMLSKLARSLV 125

Query: 134 RPAFVGALRDAKTPAEIVTLVNDVLAPAPAA--------TPAAAAPAAAAAAAPAAAAAV 185
           R  FV +LR  +T +E V ++ D +   P +        T AA A  AA AA   A AA 
Sbjct: 126 RKDFVESLRQVETDSEAVKIILDAVEDKPKSDGGSGSEDTAAAGAAGAAGAATVGAGAAA 185

Query: 186 PAPKPEPVAPEKEPEPEVGPKHIVAVTACPTGIAHTYMAADSLVAAGERAGVVVHVETQG 245
                     +           IVAVT+C TGIAHTYMAAD+L    +  G+   VE QG
Sbjct: 186 AGASASAGIDDSGSAKVDDAVRIVAVTSCATGIAHTYMAADALTQTAKDKGIDFAVEPQG 245

Query: 246 SSGSTPLAPGVIAGASAVIFATDVGVKGKERFAGKPVVASGVKRAINEPDTMITEALRAG 305
           SSG+TPL    I  A AVIFATDVGV+ K RFAGKPVV   VKR I+ P+ M+ +A++A 
Sbjct: 246 SSGTTPLTAEQIDKADAVIFATDVGVRDKGRFAGKPVVEGPVKRGIDAPEKMLDDAVKAA 305

Query: 306 MNPSAAIVDAGSAGSAADEPAGSIG--WGTHLRQVLLTGVSYMIPFVAAGGLLIALGFLL 363
            +P+A  V A S         G  G  W   L++ +++GVSYMIPFVAAGGLL+ALGFL 
Sbjct: 306 RDPNATRVKAASGSGEESASGGGKGEHWARTLQRGVMSGVSYMIPFVAAGGLLMALGFLF 365

Query: 364 GGYEISGPAEDIVLSNSLGQLP-------EG---------------GLATYLGAVLFQLG 401
           GGY+++G  +DIV + SL  LP       EG               G+  Y+G V F +G
Sbjct: 366 GGYDMAGVYQDIVTTYSLTDLPPQLFTDGEGLVAAGASGAEALDRTGMMLYMGVVFFAIG 425

Query: 402 SLAFSFLVPALAGYIAFAIADRPGLAPGFTAGAVAVFVGAGFIGGLVGGLIAGVVALWIS 461
             A SF++P L+GYIA  IADRPGLAPGF  GA+++ + AGF+G L+ G++AG +  W+S
Sbjct: 426 QAAMSFMIPVLSGYIAMGIADRPGLAPGFVGGAISLTLDAGFLGALITGILAGFLMRWMS 485

Query: 462 RIPVPQWLRGLMPVVIIPLFATLIVGALMFLVLGRPLASITSGLTNWLNGLSGSSVIFLG 521
              VP WLRGLMPVV+ PL  +LI+G +MFL+LG+P+A +   LT+ L+ +SGSS I LG
Sbjct: 486 SWSVPSWLRGLMPVVLFPLLGSLIIGLVMFLLLGQPIAWLMETLTDGLSSMSGSSAILLG 545

Query: 522 IILGLMMCFDLGGPVNKAAYAFAVAGLNVNDPASLRIMAAVMAAGMVPPLAMALASTVLR 581
           +ILGLMMCFDLGGPVNKAAY FA AGL V++P++LRIMAAVMAAGMVPP+A+++A T +R
Sbjct: 546 LILGLMMCFDLGGPVNKAAYVFATAGLVVDEPSTLRIMAAVMAAGMVPPIALSIA-TFVR 604

Query: 582 PSLFSEAERENGKAAWLLGSAFISEGAIPFAAADPLRVIPSMMAGGAVTGALIMAFDVTL 641
             LF+ AERENG+AAWLLG +FISEGAIPFAAADPLRVIPSMM GGA TGAL MAF V  
Sbjct: 605 KHLFTPAERENGRAAWLLGLSFISEGAIPFAAADPLRVIPSMMLGGATTGALSMAFSVES 664

Query: 642 SAPHGGIFVFFAIGNLLWFLVALAAGVVVAALCVVGAK 679
            APHGGIFV FAI  +  + V++ AGVVV+ + VV AK
Sbjct: 665 YAPHGGIFVIFAIHPIWGYFVSILAGVVVSTIAVVIAK 702


Lambda     K      H
   0.320    0.136    0.395 

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: 1379
Number of extensions: 66
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: 700
Length of database: 726
Length adjustment: 39
Effective length of query: 661
Effective length of database: 687
Effective search space:   454107
Effective search space used:   454107
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 (21.8 bits)
S2: 55 (25.8 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