GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TAT in Klebsiella michiganensis M5al

Align tryptophan permease (characterized)
to candidate BWI76_RS19685 BWI76_RS19685 lysine transporter

Query= CharProtDB::CH_091156
         (592 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS19685 BWI76_RS19685 lysine
           transporter
          Length = 489

 Score =  271 bits (694), Expect = 3e-77
 Identities = 148/429 (34%), Positives = 237/429 (55%), Gaps = 5/429 (1%)

Query: 74  DTSNLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHG 133
           +   L+R LK RHL MIAIGGSIGTGLFV SG  I++ GP G ++ + + G  +   +  
Sbjct: 9   EAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYILIGLMVYFLMTS 68

Query: 134 LGEITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSI 193
           LGE+    PV G+FA YG  +++    F +   Y   W   + ++++AA + + YW    
Sbjct: 69  LGELAAFMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMTYWFPDA 128

Query: 194 DPVIWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICGGGPDHEFI 253
              +W A+F  ++  +N   V+GFGEAE+ FS IK  TV  FII+ V++I G     +  
Sbjct: 129 PGWVWSALFLGIMFLLNWISVKGFGEAEYWFSLIKVATVIIFIIVGVMMIFGIFKGAQPA 188

Query: 254 GAKYW-HDPGCLANGFPGVLSVLVVASYSLGGIEMTCLASGETD--PKGLPSAIKQVFWR 310
           G   W  D    A GF  ++ V ++  +S  G E+  +A+GE++   K +P A++QVFWR
Sbjct: 189 GWSNWVIDDAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESENPEKNIPRAVRQVFWR 248

Query: 311 ILFFFLISLTLVGFLVPYTNQNLLGG--SSVDNSPFVIAIKLHHIKALPSIVNAVILISV 368
           IL F++ ++ ++  ++PYT+ +LL      +  SPF +  +   + +  +I+NAVIL +V
Sbjct: 249 ILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAIMNAVILTAV 308

Query: 369 LSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSGSMS 428
           LS GNS ++AS+R L ++A  G  P  F  + + G P   + A ++   L FL       
Sbjct: 309 LSAGNSGMYASTRMLYTLACDGKAPRIFSKLSKGGVPRNALYATTVIAGLCFLSSMFGNQ 368

Query: 429 EVFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKSLDELEFVSAVGIWGSAYSALIN 488
            V+ WL+  +G+   I WL I +SH RFR     QG  L++L + S     G  ++ ++ 
Sbjct: 369 TVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGNDLNDLPYRSGFFPLGPIFAFVLC 428

Query: 489 CLILIAQFY 497
            +I + Q Y
Sbjct: 429 LIITLGQNY 437


Lambda     K      H
   0.326    0.141    0.447 

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: 793
Number of extensions: 43
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: 592
Length of database: 489
Length adjustment: 35
Effective length of query: 557
Effective length of database: 454
Effective search space:   252878
Effective search space used:   252878
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 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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