Alignments for a candidate for tdcC in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for tdcC in Klebsiella michiganensis M5al

Align Threonine/serine transporter TdcC; H(+)/threonine-serine symporter (characterized)
to candidate BWI76_RS14475 BWI76_RS14475 serine/threonine transporter

Query= SwissProt::P0AAD8
         (443 letters)



>FitnessBrowser__Koxy:BWI76_RS14475
          Length = 427

 Score =  448 bits (1152), Expect = e-130
 Identities = 225/431 (52%), Positives = 301/431 (69%), Gaps = 16/431 (3%)

Query: 13  KQSSWRKSDTTWTLGLFGTAIGAGVLFFPIRAGFGGLIPILLMLVLAYPIAFYCHRALAR 72
           + S WRKSDT W LGL+GTAIGAGVLF PI AG GGLIP+++M +LA+P+ F+ HR L R
Sbjct: 12  ESSGWRKSDTVWMLGLYGTAIGAGVLFLPINAGVGGLIPLIIMAILAFPMTFFAHRGLTR 71

Query: 73  LCLSGSNPSGNITETVEEHFGKTGGVVITFLYFFAICPLLWIYGVTITNTFMTFWENQLG 132
             LSG NP  +ITE VEEHFG   G +IT LYFFAI P+L +Y V ITNT  +F  +QLG
Sbjct: 72  FVLSGKNPGEDITEVVEEHFGTGAGKLITLLYFFAIYPILLVYSVAITNTVDSFITHQLG 131

Query: 133 FAPLNRGFVALFLLLLMAFVIWFGKDLMVKVMSYLVWPFIASLVLISLSLIPYWNSAVID 192
                R  ++L L++ M  ++ FG+ ++VK MS LV+PF+ +L++++L LIP WN AV+D
Sbjct: 132 LVSPPRAILSLILIVGMMGIVRFGEKMIVKAMSVLVFPFVFALMILALYLIPQWNGAVLD 191

Query: 193 QVDLGSLSLTGHDGILITVWLGISIMVFSFNFSPIVSSFVVSKREEYEKDFGRDFTERKC 252
            + L   S TG +G+ +T+WL I +MVFSFN SPI+SSF V+KREEY +D      ERKC
Sbjct: 192 TLSLSGASATG-NGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGED-----AERKC 245

Query: 253 SQIISRASMLMVAVVMFFAFSCLFTLSPANMAEAKAQNIPVLSYLANHFASMTGTKTTFA 312
           S+I+  A ++MV  VMFF FSC+ +LSP N+AEAKAQNI +LSYLANHF          A
Sbjct: 246 SRILGFAHIMMVLTVMFFVFSCVLSLSPENLAEAKAQNISILSYLANHFN---------A 296

Query: 313 ITLEYAASIIALVAIFKSFFGHYLGTLEGLNGLVLKFGYKGDKTKVSLGKLNTISMIFIM 372
             + + A IIA++AI KSF GHYLG  EG NG+V+K   +G    + + KLN I+ +F++
Sbjct: 297 PVIAWMAPIIAMIAITKSFLGHYLGAREGFNGMVIK-SLRGKGKSIEINKLNKITALFML 355

Query: 373 GSTWVVAYANPNILDLIEAMGAPIIASLLCLLPMYAIRKAPSLAKYRGRLDNVFVTVIGL 432
            +TW+VA  NP+IL +IE +G P+IA +L L+PMYAI K P++ KY G + N FV V+GL
Sbjct: 356 VTTWIVATLNPSILGMIETLGGPVIAMILFLMPMYAINKVPAMRKYSGHISNAFVVVMGL 415

Query: 433 LTILNIVYKLF 443
           + I  I + LF
Sbjct: 416 IAISAIFFSLF 426


Lambda     K      H
   0.328    0.141    0.430 

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: 605
Number of extensions: 34
Number of successful extensions: 7
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: 443
Length of database: 427
Length adjustment: 32
Effective length of query: 411
Effective length of database: 395
Effective search space:   162345
Effective search space used:   162345
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)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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