GapMind for catabolism of small carbon sources

 

Alignments for a candidate for citA in Pseudomonas fluorescens FW300-N2E3

Align citrate transporter (characterized)
to candidate AO353_25075 AO353_25075 citrate-proton symporter

Query= CharProtDB::CH_014606
         (431 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25075
          Length = 432

 Score =  622 bits (1603), Expect = 0.0
 Identities = 296/414 (71%), Positives = 352/414 (85%)

Query: 6   SRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLM 65
           S+    GAILRVTSGNFLEQFDFFLFGFYATYI++TFFP  SEFA+LM+TFAVFGSGFLM
Sbjct: 11  SKGSKLGAILRVTSGNFLEQFDFFLFGFYATYISQTFFPTTSEFASLMMTFAVFGSGFLM 70

Query: 66  RPIGAVVLGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQG 125
           RP+GA+VLGAYID++GRRKGL++TL+IM  GT+LIALVPGY +IG+ AP+LVL+GRLLQG
Sbjct: 71  RPLGAIVLGAYIDKVGRRKGLIVTLSIMAAGTVLIALVPGYASIGIAAPILVLLGRLLQG 130

Query: 126 FSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDEISEW 185
           FSAG E+GGVSVYL+EIATPG +GFYTSWQSASQQVAI++AA +GY +N ++   +++ W
Sbjct: 131 FSAGAEMGGVSVYLAEIATPGRRGFYTSWQSASQQVAIILAAALGYTINASMEAADVAAW 190

Query: 186 GWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNWRIITAGTLLVA 245
           GWRIPFFIGC+IIP IF++RRSLQET+AF  R H P   E+F ++  NWR + AG LL +
Sbjct: 191 GWRIPFFIGCLIIPFIFIIRRSLQETDAFKARSHHPSASEVFRSMRDNWRTVLAGGLLAS 250

Query: 246 MTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRRPVLM 305
           MTTTTFY ITVYTPT+GR+VLNLS  DSLVVT+ VG+SNFIWLPIGG ISDRIGRRP+L+
Sbjct: 251 MTTTTFYLITVYTPTFGRSVLNLSTSDSLVVTLFVGLSNFIWLPIGGTISDRIGRRPLLL 310

Query: 306 GITLLALVTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTVG 365
            +TLL + T  P M+WL AA  F R+  VLL+FSFFFG+YNGAMVAALTEVMP  VR VG
Sbjct: 311 AVTLLCIFTAYPAMHWLAAAASFERLLAVLLYFSFFFGIYNGAMVAALTEVMPQNVRVVG 370

Query: 366 FSLAFSLATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGLAATTMLFAR 419
           FSLAFSLATA+FGG TPA+ST LVQ TGDK+SP +WLM AALCG  ATT+L+ R
Sbjct: 371 FSLAFSLATAVFGGFTPAVSTILVQATGDKASPAYWLMFAALCGFTATTILYRR 424


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: 643
Number of extensions: 21
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: 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