GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-ABC in Williamsia sterculiae CPCC 203464

Align The fructose-specific PTS Enzyme IIABC FruA (characterized)
to candidate WP_076477611.1 BW971_RS05975 PTS transporter subunit EIIA

Query= TCDB::Q0S1N2
         (700 letters)



>NCBI__GCF_900156495.1:WP_076477611.1
          Length = 684

 Score =  878 bits (2268), Expect = 0.0
 Identities = 469/679 (69%), Positives = 531/679 (78%), Gaps = 35/679 (5%)

Query: 14  IISEDLISLDTDLGASKEDVISALSRRLADAGRATEADALRDAALARESQSATGLPGGIA 73
           II+ DL++LD D GA K +VI  L  RLA  GR  +  A+ +AA+ARE+QSATGLPGGIA
Sbjct: 5   IITTDLVALDVDAGAEKSEVIDFLVERLAADGRVHDTVAVNEAAMAREAQSATGLPGGIA 64

Query: 74  IPHCRSEAVVAASLGFARLAPKVDFGAPDGPADLVFLIAAPEGAGAEHMKLLSSLARALV 133
           IPHCR+E V AA L FARLAP VDFGA DGPADLVFLIAAP   G++HMKLLSSLARALV
Sbjct: 65  IPHCRTEGVSAAGLSFARLAPAVDFGAKDGPADLVFLIAAPASGGSQHMKLLSSLARALV 124

Query: 134 RPAFVGALRDAKTPAEIVTLVNDVLAPAPAATPAAAAPAAAAAAAPAAAAAVPAPKPEPV 193
           RP FV +LR+AK+  E+V LV+  + PAPA +PAAAA  AA+  APA AA          
Sbjct: 125 RPDFVTSLRNAKSADEVVALVDQAINPAPATSPAAAAVPAASGGAPAKAAT--------- 175

Query: 194 APEKEPEPEVGPKHIVAVTACPTGIAHTYMAADSLVAAGERAGVVVHVETQGSSGSTPLA 253
                         +VA+TACPTGIAHTYMAAD+L  A ERAGV + VETQGSS +TP  
Sbjct: 176 -------------RLVAITACPTGIAHTYMAADALKFAAERAGVDLVVETQGSSANTPTD 222

Query: 254 PGVIAGASAVIFATDVGVKGKERFAGKPVVASGVKRAINEPDTMITEALRAGMNPSAAIV 313
           P VI  A AVIFATDVGVK ++RFAGKPV+ASGVKRAINEPD MI EA+ A  +P A+ V
Sbjct: 223 PSVIRDADAVIFATDVGVKNRDRFAGKPVIASGVKRAINEPDVMIAEAVAAAGDPDASRV 282

Query: 314 DAGSAGSA-ADEPAGSIGWGTHLRQVLLTGVSYMIPFVAAGGLLIALGFLLGGYEIS--- 369
              +A +A A    G +GWGT LRQVLLTGVSYMIPFVAAGGLLIALGFLLGGY+I+   
Sbjct: 283 GGDTAAAATASTAGGDLGWGTRLRQVLLTGVSYMIPFVAAGGLLIALGFLLGGYKIALAP 342

Query: 370 -GPAED-------IVLSNSLGQLPEGGLATYLGAVLFQLGSLAFSFLVPALAGYIAFAIA 421
            G A+        I LSNSL  LP GGLA YLGA+ F LG LAFSFLVPALAGYIA+AIA
Sbjct: 343 PGSADGTEAIGKTIALSNSLWNLPSGGLAQYLGAICFTLGGLAFSFLVPALAGYIAYAIA 402

Query: 422 DRPGLAPGFTAGAVAVFVGAGFIGGLVGGLIAGVVALWISRIPVPQWLRGLMPVVIIPLF 481
           DRPGLAPGFTAGAVAVFVGAGFIGGLVGGL+ G VALW+ RIP+P W RGLMPVVIIPL 
Sbjct: 403 DRPGLAPGFTAGAVAVFVGAGFIGGLVGGLLGGFVALWVGRIPLPAWARGLMPVVIIPLL 462

Query: 482 ATLIVGALMFLVLGRPLASITSGLTNWLNGLSGSSVIFLGIILGLMMCFDLGGPVNKAAY 541
           ATL  G +MFL LGRPLA + + LT+WLNGLSG+S I LGIILGLMMCFDLGGPVNKAAY
Sbjct: 463 ATLATGGIMFLFLGRPLAWVNTSLTDWLNGLSGTSAIILGIILGLMMCFDLGGPVNKAAY 522

Query: 542 AFAVAGLNVNDPASLRIMAAVMAAGMVPPLAMALASTVLRPSLFSEAERENGKAAWLLGS 601
           AFAV GL+  DPA LRIMAAVMAAGMVPPLA+ALA T LRP LF+E ERENGKAAWLLG+
Sbjct: 523 AFAVQGLSSGDPAQLRIMAAVMAAGMVPPLALALA-TALRPRLFTEPERENGKAAWLLGA 581

Query: 602 AFISEGAIPFAAADPLRVIPSMMAGGAVTGALIMAFDVTLSAPHGGIFVFFAIGNLLWFL 661
           +FISEGAIPFAA DPLRVIPSMMAGGAVTGAL+MAFDVTL APHGGIFVFFA+GN+  FL
Sbjct: 582 SFISEGAIPFAAVDPLRVIPSMMAGGAVTGALVMAFDVTLRAPHGGIFVFFAMGNVFGFL 641

Query: 662 VALAAGVVVAALCVVGAKE 680
           ++L  G+V++A  V+  K+
Sbjct: 642 LSLLVGMVISATLVLALKQ 660


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: 1382
Number of extensions: 70
Number of successful extensions: 6
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: 684
Length adjustment: 39
Effective length of query: 661
Effective length of database: 645
Effective search space:   426345
Effective search space used:   426345
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: 54 (25.4 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