Aligments for a candidate for citA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
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, or view the source code.

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