Alignments for a candidate for sdc in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdc in Klebsiella michiganensis M5al

Align Dicarboxylate (succinate, fumarate, malate) transporter, vcINDY (characterized)
to candidate BWI76_RS24195 BWI76_RS24195 anion transporter

Query= TCDB::Q9KNE0
         (462 letters)



>FitnessBrowser__Koxy:BWI76_RS24195
          Length = 462

 Score =  739 bits (1907), Expect = 0.0
 Identities = 364/461 (78%), Positives = 416/461 (90%)

Query: 1   MNRNDSVPLPTNTREWFLHRNSLIVLADVALFLALYHFLPFEHNVVLGISMLAFIAVLWL 60
           MN+ND  PLPTNT EWF +RNS+I+L D+ LF+ LY+ LP+E  VV+G+SMLAFIAVLWL
Sbjct: 1   MNKNDMSPLPTNTHEWFFNRNSIIILLDIVLFIVLYNTLPYEPKVVMGLSMLAFIAVLWL 60

Query: 61  TEALHVTVTAILVPVMAVFFGIFETQAALNNFANSIIFLFLGGFALAAAMHHQGLDKVIA 120
           TEALHVTVTAI+VPVMAV  G+F TQAALN+FANS IFLFLGGFALAAAMH QGLDKVIA
Sbjct: 61  TEALHVTVTAIMVPVMAVLLGVFNTQAALNSFANSTIFLFLGGFALAAAMHVQGLDKVIA 120

Query: 121 DKVLAMAQGKMSVAVFMLFGVTALLSMWISNTATAAMMLPLVLGVLSKVDADKQRSTYVF 180
           DKVLAMA+GKMS+AVFMLFGVTALLSMWISNTATAAMM+PLVLG+LSKVD+    STYVF
Sbjct: 121 DKVLAMARGKMSLAVFMLFGVTALLSMWISNTATAAMMMPLVLGILSKVDSKNSHSTYVF 180

Query: 181 VLLGVAYSASIGGIATLVGSPPNAIAAAEVGLSFTDWMKFGLPTAMMMLPMAIAILYFLL 240
           VLLG+AYSASIGG+AT+VGSPPNAIAAAEVGLSF DWMKFG P  +++LP+AIAILY + 
Sbjct: 181 VLLGIAYSASIGGMATIVGSPPNAIAAAEVGLSFFDWMKFGFPAMIVLLPVAIAILYLVF 240

Query: 241 KPTLNGMFELDRAPVNWDKGKVVTLGIFGLTVFLWIFSSPINAALGGFKSFDTLVALGAI 300
           +P L G FE +   V+WDKGK+VTL IF LTVF WIFS PIN  LGGFKSFDT+VALGAI
Sbjct: 241 RPELKGTFETNSERVDWDKGKIVTLAIFALTVFFWIFSGPINDLLGGFKSFDTIVALGAI 300

Query: 301 LMLSFARVVHWKEIQKTADWGVLLLFGGGLCLSNVLKQTGTSVFLANALSDMVSHMGIFV 360
           ++++FARVVHWK+I+KTADWGVLLLFGGG+CLSNVLK+TGTS+FLAN +S MV+HMGIF+
Sbjct: 301 ILVNFARVVHWKDIEKTADWGVLLLFGGGICLSNVLKETGTSLFLANQISGMVAHMGIFI 360

Query: 361 VILVVATFVVFLTEFASNTASAALLIPVFATVAEAFGMSPVLLSVLIAVAASCAFMLPVA 420
           +ILV+ATFVVFLTEFASNTASAALLIPVFA+VAEAFGMSPV+LSVLIA+AASCAFMLPVA
Sbjct: 361 IILVIATFVVFLTEFASNTASAALLIPVFASVAEAFGMSPVILSVLIAIAASCAFMLPVA 420

Query: 421 TPPNAIVFASGHIKQSEMMRVGLYLNIACIGLLTAIAMLFW 461
           TPPNAIVFA+GHIKQ EMMR GL+LNIACI +LT  +MLFW
Sbjct: 421 TPPNAIVFATGHIKQQEMMRAGLFLNIACIIVLTGFSMLFW 461



 Score = 39.7 bits (91), Expect = 2e-07
 Identities = 37/147 (25%), Positives = 67/147 (45%), Gaps = 9/147 (6%)

Query: 323 LLLFGGGLCLSNVLKQTGTSVFLANALSDMV-SHMGIFVVILVVATFVVFLTEFASNTAS 381
           + LF GG  L+  +   G    +A+ +  M    M + V +L   T    L+ + SNTA+
Sbjct: 97  IFLFLGGFALAAAMHVQGLDKVIADKVLAMARGKMSLAVFMLFGVT--ALLSMWISNTAT 154

Query: 382 AALLIPVFATV---AEAFGMSPVLLSVLIAVAASCAF---MLPVATPPNAIVFASGHIKQ 435
           AA+++P+   +    ++       + VL+ +A S +       V +PPNAI  A   +  
Sbjct: 155 AAMMMPLVLGILSKVDSKNSHSTYVFVLLGIAYSASIGGMATIVGSPPNAIAAAEVGLSF 214

Query: 436 SEMMRVGLYLNIACIGLLTAIAMLFWQ 462
            + M+ G    I  + +  AI  L ++
Sbjct: 215 FDWMKFGFPAMIVLLPVAIAILYLVFR 241


Lambda     K      H
   0.329    0.139    0.417 

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: 753
Number of extensions: 38
Number of successful extensions: 4
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: 462
Length of database: 462
Length adjustment: 33
Effective length of query: 429
Effective length of database: 429
Effective search space:   184041
Effective search space used:   184041
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources