GapMind for catabolism of small carbon sources

 

Alignments for a candidate for STP6 in Klebsiella michiganensis M5al

Align sugar transport protein 6 (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter

Query= CharProtDB::CH_091493
         (507 letters)



>FitnessBrowser__Koxy:BWI76_RS24055
          Length = 464

 Score =  218 bits (556), Expect = 3e-61
 Identities = 150/471 (31%), Positives = 247/471 (52%), Gaps = 34/471 (7%)

Query: 18  TVYVFICVMIAAVGGLIFGYDIGISGGVSAMDDFLKEFFPAVWERKKHVHENNYCKYDNQ 77
           T+  F+C  +AA+ GL+FG DIG+  G  A+     EF     +   H  E         
Sbjct: 13  TMTFFVC-FLAALAGLLFGLDIGVIAG--ALPFIANEF-----QISAHTQE--------- 55

Query: 78  FLQLFTSSLYLAALVASFVASATCSKLGRRPTMQFASIFFLIGVGLTAGAVNLVMLIIGR 137
                 SS+   A V +  +     KLGR+ ++   +I F+ G   +A A N+ +L+I R
Sbjct: 56  ---WVVSSMMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLLISR 112

Query: 138 LFLGFGVGFGNQAVPLFLSEIAPAQLRGGLNIVFQLMVTIGILIANIVNYFTATVHPYGW 197
           + LG  VG  +   PL+LSEIAP ++RG +  ++QLM+TIGIL A + +  TA  +   W
Sbjct: 113 VLLGLAVGVASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSD--TAFSYSGAW 170

Query: 198 RIALGGAGIPAVILLFGSLLIIETPTSLIERNKNEEGKEALRKIRGVDDINDEYESIVHA 257
           R  LG   IPAV+LL G + + ++P     + +  + +  L ++R   D + E +  +  
Sbjct: 171 RWMLGVIIIPAVLLLIGVVFLPDSPRWFAAKRRFVDAERVLLRLR---DTSAEAKRELDE 227

Query: 258 CDIASQVKDPYRKLLKPAS--RPPFIIGMLLQLFQQFTGINAIMFYAPVLFQTVGFGSDA 315
              + +VK     L K  S  R    +G+LLQ+ QQFTG+N IM+YAP +F+  G+ +  
Sbjct: 228 IRESLKVKQSGWSLFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTT 287

Query: 316 -ALLSAVITGSINVLATFVGIYLVDRTGRRFLLLQSSVHMLICQLIIGIILAKDLGVTGT 374
             +   VI G  NVLATF+ I LVDR GR+  L+   + M +   I+G ++   +G+   
Sbjct: 288 EQMWGTVIVGLTNVLATFIAIGLVDRWGRKPTLILGFIVMALGMGILGSMM--HIGIHSA 345

Query: 375 LGRPQALVVVIFVCVYVMGFAWSWGPLGWLIPSETFPLETRSAGFAVAVSCNMFFTFVIA 434
             +      V+ + ++++GFA S GPL W++ SE  PL+ R  G   + + N     ++ 
Sbjct: 346 TAQ---YFAVLMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVG 402

Query: 435 QAFLSMLCGMRSGIFFFFSGWIIVMGLF-AFFFIPETKGIAIDDMRESVWK 484
             FL+ML  + S   F+  G + ++ +F   + IPETK ++++ +  ++ K
Sbjct: 403 ATFLTMLNSLGSANTFWVYGGLNILFIFLTLWLIPETKNVSLEHIERNLMK 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: 611
Number of extensions: 33
Number of successful extensions: 8
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: 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.

Links

Downloads

Related tools

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