GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaC in Klebsiella michiganensis M5al

Align Serine transporter (characterized)
to candidate BWI76_RS22875 BWI76_RS22875 serine transporter

Query= SwissProt::P0AAD6
         (429 letters)



>FitnessBrowser__Koxy:BWI76_RS22875
          Length = 429

 Score =  787 bits (2033), Expect = 0.0
 Identities = 400/429 (93%), Positives = 415/429 (96%)

Query: 1   METTQTSTIASKDSRSAWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILA 60
           METTQTSTI S  +RS WRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILA
Sbjct: 1   METTQTSTIVSDATRSGWRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILA 60

Query: 61  FPMTFFAHRGLTRFVLSGKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAI 120
           FPMTFFAHRG+TRFVLSGKNPGEDITEVVEEHFG+GAGKLITLLYFFAIYPILLVYSVAI
Sbjct: 61  FPMTFFAHRGMTRFVLSGKNPGEDITEVVEEHFGVGAGKLITLLYFFAIYPILLVYSVAI 120

Query: 121 TNTVESFMSHQLGMTPPPRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLA 180
           TNTVESFM HQL +TPPPRAILSLILIVGMMTIVRFGEQMIVKAMS+LVFPFV  LM+LA
Sbjct: 121 TNTVESFMLHQLHITPPPRAILSLILIVGMMTIVRFGEQMIVKAMSVLVFPFVVALMILA 180

Query: 181 LYLIPQWNGAALETLSLDTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG 240
            YLIPQWNGAALETLSL +A+ATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG
Sbjct: 181 FYLIPQWNGAALETLSLSSATATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYG 240

Query: 241 DMAEQKCSKILAFAHIMMVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPV 300
             AE+KCS ILA AHIMMVLTVMFFVFSCVLSL+PADLAAAK+QNISILSYLANHFNAPV
Sbjct: 241 QGAEKKCSSILARAHIMMVLTVMFFVFSCVLSLSPADLAAAKDQNISILSYLANHFNAPV 300

Query: 301 IAWMAPIIAIIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTT 360
           IAWMAPIIA+IAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLN+ITALFMLVTT
Sbjct: 301 IAWMAPIIAMIAITKSFLGHYLGAREGFNGMVIKSLRGKGKSIEINKLNKITALFMLVTT 360

Query: 361 WIVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAI 420
           WIVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGH+SNVFVV+MGLIAI
Sbjct: 361 WIVATLNPSILGMIETLGGPIIAMILFLMPMYAIQKVPAMRKYSGHVSNVFVVIMGLIAI 420

Query: 421 SAIFYSLFS 429
           SAIFYSLFS
Sbjct: 421 SAIFYSLFS 429


Lambda     K      H
   0.328    0.140    0.416 

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: 833
Number of extensions: 27
Number of successful extensions: 1
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: 429
Length of database: 429
Length adjustment: 32
Effective length of query: 397
Effective length of database: 397
Effective search space:   157609
Effective search space used:   157609
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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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