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_RS03110 BWI76_RS03110 MFS transporter

Query= CharProtDB::CH_091493
         (507 letters)



>FitnessBrowser__Koxy:BWI76_RS03110
          Length = 499

 Score =  194 bits (494), Expect = 5e-54
 Identities = 141/486 (29%), Positives = 234/486 (48%), Gaps = 34/486 (6%)

Query: 3   VVVSNANAPAFEAKMTVYVFICVMIAAVGGLIFGYDIGISGGVSAMDDFLKEFFPAVWER 62
           + ++ A+ P  E   T +V +  +IA +GGL+FGYD G+  G             A+   
Sbjct: 7   LTLNKASGPNSETPTTPFVKVVALIATLGGLLFGYDTGVISG-------------ALLFM 53

Query: 63  KKHVHENNYCKYDNQFLQLFTSSLYLAALVASFVASATCSKLGRRPTMQFASIFFLIGVG 122
              +H   +         L TSSL   A   + ++    +  GR+  + + ++ F IG  
Sbjct: 54  GTELHLTPFTT------GLVTSSLLFGAAFGALLSGNLANAAGRKKIILWLAVLFAIGAI 107

Query: 123 LTAGAVNLVMLIIGRLFLGFGVGFGNQAVPLFLSEIAPAQLRGGLNIVFQLMVTIGILIA 182
            T+ A ++  +I  RL LG  VG     VP++++EIAPA  RG L  + +LM+  G L+A
Sbjct: 108 GTSMAPDVNWMIFFRLILGVAVGGAAATVPVYIAEIAPANKRGQLVTLQELMIVSGQLLA 167

Query: 183 NIVNYFTATVHPYG-----WRIALGGAGIPAVILLFGSLLIIETPTSLIERNKNEEGKEA 237
            I N   AT H        WR  L  A +PAV+L FG + + ++P     + +  E +  
Sbjct: 168 YISN---ATFHEVWGGESTWRWMLAVATLPAVLLWFGMMFMPDSPRWYAMKGRLAEARRV 224

Query: 238 LRKIRGVDDINDEYESIVHACDIASQVKDP-YRKLLKPASRPPFIIGMLLQLFQQFTGIN 296
           L + R  DD+  E   I    D    +  P + +++ P     F+IG+ + + QQ TG+N
Sbjct: 225 LERTRHKDDVEWELLEITETLDEQRNLGKPRFSEIMTPWLFKLFMIGIGIAVIQQLTGVN 284

Query: 297 AIMFYAPVLFQTVGFGSDAALLSAVITGSINVLATFVGIYLVDRTGRRFLLLQSSVHMLI 356
            IM+YAP +  +VG   +AAL + +  G ++VL TFVGI+++ + GRR + +        
Sbjct: 285 TIMYYAPTVLTSVGMTDNAALFATIANGVVSVLMTFVGIWMLGKIGRRPMTMIGQFGCTA 344

Query: 357 CQLIIGIILAKDLGVTGTLGRPQALVVVIFVCVYVMGFAWSWG---PLGWLIPSETFPLE 413
           C + IG +    L      G+P AL   + +   ++  ++  G   P+ WL+ SE FP  
Sbjct: 345 CLVFIGAV--SYLLPETVNGQPDALRAYMVLAGMLLFLSFQQGALSPVTWLLMSEIFPTR 402

Query: 414 TRSAGFAVAVSCNMFFTFVIAQAFLSMLCGM-RSGIFFFFSGWIIVMGLFAFFFIPETKG 472
            R      AV       F+I+  F  +L  +  SG FF F+G  +   +F    +PET+ 
Sbjct: 403 LRGIFMGGAVFSMWIANFLISLFFPILLAWLGLSGTFFIFAGIGVFGAIFVIKCVPETRH 462

Query: 473 IAIDDM 478
            +++ +
Sbjct: 463 RSLEQI 468


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: 597
Number of extensions: 33
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 507
Length of database: 499
Length adjustment: 34
Effective length of query: 473
Effective length of database: 465
Effective search space:   219945
Effective search space used:   219945
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