GapMind for catabolism of small carbon sources

 

Alignments for a candidate for STP6 in Escherichia coli BW25113

Align sugar transport protein 6 (characterized)
to candidate 17022 b2943 D-galactose transporter (NCBI)

Query= CharProtDB::CH_091493
         (507 letters)



>FitnessBrowser__Keio:17022
          Length = 464

 Score =  209 bits (533), Expect = 1e-58
 Identities = 148/473 (31%), Positives = 241/473 (50%), Gaps = 46/473 (9%)

Query: 22  FICVMIAAVGGLIFGYDIGISGGVSAMDDFLKEFFPAVWERKKHVHENNYCKYDNQFLQL 81
           F+C  +AA+ GL+FG DIG+  G  A+     EF     +   H  E             
Sbjct: 17  FVC-FLAALAGLLFGLDIGVIAG--ALPFIADEF-----QITSHTQE------------W 56

Query: 82  FTSSLYLAALVASFVASATCSKLGRRPTMQFASIFFLIGVGLTAGAVNLVMLIIGRLFLG 141
             SS+   A V +  +     KLGR+ ++   +I F+ G   +A A N+ +LI+ R+ LG
Sbjct: 57  VVSSMMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLG 116

Query: 142 FGVGFGNQAVPLFLSEIAPAQLRGGLNIVFQLMVTIGILIANIVNYFTATVHPYGWRIAL 201
             VG  +   PL+LSEIAP ++RG +  ++QLM+TIGIL A + +  TA  +   WR  L
Sbjct: 117 LAVGVASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSD--TAFSYTGAWRWML 174

Query: 202 GGAGIPAVILLFGSLLIIETPTSLIERNKNEEGKEALRKIRGVDDINDEYESIVHACDIA 261
           G   IPA++LL G   + ++P     + +  + +  L ++R   D + E +  +     +
Sbjct: 175 GVIIIPAILLLIGVFFLPDSPRWFAAKRRFVDAERVLLRLR---DTSAEAKRELDEIRES 231

Query: 262 SQVKDPYRKLLKPAS--RPPFIIGMLLQLFQQFTGINAIMFYAPVLFQTVGF-GSDAALL 318
            QVK     L K  S  R    +G+LLQ+ QQFTG+N IM+YAP +F+  G+  +   + 
Sbjct: 232 LQVKQSGWALFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMW 291

Query: 319 SAVITGSINVLATFVGIYLVDRTGRRFLLLQSSVHMLICQLIIGIILAKDLGVTGT---- 374
             VI G  NVLATF+ I LVDR GR+  L               +++A  +GV GT    
Sbjct: 292 GTVIVGLTNVLATFIAIGLVDRWGRKPTLTLGF-----------LVMAAGMGVLGTMMHI 340

Query: 375 -LGRPQA-LVVVIFVCVYVMGFAWSWGPLGWLIPSETFPLETRSAGFAVAVSCNMFFTFV 432
            +  P A    +  + ++++GFA S GPL W++ SE  PL+ R  G   + + N     +
Sbjct: 341 GIHSPSAQYFAIAMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMI 400

Query: 433 IAQAFLSMLCGM-RSGIFFFFSGWIIVMGLFAFFFIPETKGIAIDDMRESVWK 484
           +   FL+ML  +  +  F+ ++   ++  L   + +PETK ++++ +  ++ K
Sbjct: 401 VGATFLTMLNTLGNANTFWVYAALNVLFILLTLWLVPETKHVSLEHIERNLMK 453


Lambda     K      H
   0.329    0.144    0.446 

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: 594
Number of extensions: 34
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 507
Length of database: 464
Length adjustment: 34
Effective length of query: 473
Effective length of database: 430
Effective search space:   203390
Effective search space used:   203390
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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