GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citA in Herbaspirillum seropedicae SmR1

Align citrate transporter (characterized)
to candidate HSERO_RS07330 HSERO_RS07330 major facilitator transporter

Query= CharProtDB::CH_014606
         (431 letters)



>FitnessBrowser__HerbieS:HSERO_RS07330
          Length = 432

 Score =  573 bits (1478), Expect = e-168
 Identities = 270/416 (64%), Positives = 339/416 (81%)

Query: 2   TQQPSRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGS 61
           T   ++      +LRVTSGNFLE FDFFL+GFYA+YI+KTFFP+++EF +L+LTF  FG+
Sbjct: 4   TTTNAKHSKLSTVLRVTSGNFLEMFDFFLYGFYASYISKTFFPSDNEFVSLILTFGTFGA 63

Query: 62  GFLMRPIGAVVLGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGR 121
           GFLMRP+GA++LG+YIDR+GRR+GL++TLAIM  GTLLIA VPGY TIG+ AP+LVL GR
Sbjct: 64  GFLMRPLGAIILGSYIDRVGRRQGLIVTLAIMAIGTLLIAFVPGYATIGVAAPILVLTGR 123

Query: 122 LLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDE 181
           LLQGFSAGVELGGVSVYL+E+ATPGNKGFY SWQSASQQ AI+ +ALIGY ++ +L   +
Sbjct: 124 LLQGFSAGVELGGVSVYLAEMATPGNKGFYVSWQSASQQAAIMASALIGYLVSQSLSPVQ 183

Query: 182 ISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNWRIITAGT 241
           IS+WGWRIPFFIGCMI+P IF++RRSLQET+ FL RK  P   EI ++IA+NW+I+ AG 
Sbjct: 184 ISDWGWRIPFFIGCMIVPAIFIIRRSLQETDEFLARKRHPSFGEIMSSIAQNWKIVVAGM 243

Query: 242 LLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRR 301
           ++V MTT +FY ITVYTPT+G+ VL LSA DSL+VT  VG+SNF WLPI GA+SDR+GRR
Sbjct: 244 MMVVMTTVSFYLITVYTPTFGKNVLKLSASDSLIVTFCVGLSNFCWLPIMGALSDRVGRR 303

Query: 302 PVLMGITLLALVTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYV 361
           PVL+  TLL L+T  PVM+WL +   F  + +  LW SF +  YNGA V ALTEVMP +V
Sbjct: 304 PVLVAFTLLTLLTAYPVMSWLVSDISFKNLLITELWLSFLYASYNGAAVVALTEVMPAHV 363

Query: 362 RTVGFSLAFSLATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGLAATTMLF 417
           RTVGFSLA+SLATAIFGG TP +ST L++ +GDK++PG+W+  AA+CGL AT +L+
Sbjct: 364 RTVGFSLAYSLATAIFGGFTPLVSTWLIETSGDKAAPGYWMSFAAVCGLLATLVLY 419


Lambda     K      H
   0.328    0.141    0.432 

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: 630
Number of extensions: 23
Number of successful extensions: 2
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: 431
Length of database: 432
Length adjustment: 32
Effective length of query: 399
Effective length of database: 400
Effective search space:   159600
Effective search space used:   159600
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