GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sacP in Tatumella morbirosei LMG 23360

Align Sucrose porter (ScrA) (characterized)
to candidate WP_038022621.1 HA49_RS06690 PTS transporter subunit EIIC

Query= TCDB::P08470
         (456 letters)



>NCBI__GCF_000757425.2:WP_038022621.1
          Length = 624

 Score =  243 bits (620), Expect = 1e-68
 Identities = 145/455 (31%), Positives = 246/455 (54%), Gaps = 20/455 (4%)

Query: 1   MDFEQISCSLLPLLGGKENIASAAHCATRLRLVLVDDSLADQQAIGKVEGVKGCFRNAGQ 60
           MD  +++ ++L  +GG+ N+    HCATRLR  L DDS+AD  A+ K+EGV    R+ GQ
Sbjct: 1   MDLHELAKNILSAVGGESNVTQVVHCATRLRFELADDSVADIAALEKMEGVITTVRSGGQ 60

Query: 61  MQIIFGTGVVNKVYAAFTQAAGISESSKSEAADIAAKKLNPFQRIARLLSNIFVPIIPAI 120
            Q++ G  V   VY        I+   K  +AD   KK     R+  ++S+IF P++ A+
Sbjct: 61  FQVVIGNKVAG-VYKNLESMLTINNPQKKLSAD--NKKPPLISRLIDIISSIFTPLLGAM 117

Query: 121 VASGLLMGLLGMVKTYGWVDPGNAIYIMLDMCSSAAFIILPILIGFTAAREFGGNPYLGA 180
            ASG++ GLL +     W+    +  ++L   S + F  LP+L+  T+AR+F  + ++  
Sbjct: 118 AASGIIKGLLSIAFANNWLSKEESSAVILQSASDSLFYFLPVLLAITSARKFKTDVFVSV 177

Query: 181 TLGGILTHPALTNAWGVAAGFHT-MNFFGFEIAMIGYQGTVFPVLLAVWFMSIVEKQLRR 239
           T+ G L +P + N +      HT ++FFG  + M+ Y GTV PV+LAV+ MS++E  + +
Sbjct: 178 TMAGALIYPDIVNFYTQ----HTAVSFFGIPVMMMKYTGTVLPVILAVYVMSLIESIIAK 233

Query: 240 AIPDALDLILTPFLTVIISGFIALLIIGPAGRALGDGISFVLSTLISHAGWLAGLLFGGL 299
            I + +  ++ PF+ ++I   + L+ IGP G    + ++ V   + +    +A  LF   
Sbjct: 234 YIHETIRNVILPFILLLIMVPLTLMTIGPIGIYTSEAVAGVFIKIFAFNPVIASALFCAG 293

Query: 300 YSVIVITGIHHSFHAV---EAGLLGNPSIGVNFLLPIWAMANVAQGGACLAVWFKTKDAK 356
           + + VI G+H +F  V   +  +LG  ++  + +  ++     AQ GA LAV  KTKD K
Sbjct: 294 WQIFVIFGMHWAFTPVIINDISVLGRSTLKASTVPAVF-----AQSGAVLAVLLKTKDKK 348

Query: 357 IKAITLPSAFSAMLGITEAAIFGINLRFVKPFIAALIGGAAGGAWVVSVHVYMTAVGLTA 416
           +K +   +  S++ GITE A++GI L+  +PFI A+I  A GG  V   +    ++G+ +
Sbjct: 349 LKTLASGAFISSVFGITEPAVYGITLKLKRPFICAIIASAVGGGIVGYSNSAAISMGIPS 408

Query: 417 IPGMAIVQASSLLNYIIGMVIAFGVAFTVSLVLKY 451
           +  + I           G++IA   +F ++ VL Y
Sbjct: 409 LVTLPIFYGEG----FAGLLIAIATSFIIAAVLTY 439


Lambda     K      H
   0.326    0.141    0.424 

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: 694
Number of extensions: 39
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 456
Length of database: 624
Length adjustment: 35
Effective length of query: 421
Effective length of database: 589
Effective search space:   247969
Effective search space used:   247969
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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