GapMind for catabolism of small carbon sources

 

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

Align Citrate:H+ symporter (characterized)
to candidate AO353_26710 AO353_26710 citrate-proton symporter

Query= TCDB::P16482
         (444 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_26710
          Length = 434

 Score =  677 bits (1748), Expect = 0.0
 Identities = 341/436 (78%), Positives = 381/436 (87%), Gaps = 4/436 (0%)

Query: 8   MRASSTAPVRMMATAGGARIGAILRVTSGNFLEQFDFFLFGFYATYIAHTFFPASSEFAS 67
           M+A++  P    AT+  +++ AI RVTSGNFLEQFDFFLFGFYATYIA  FFPASSEFAS
Sbjct: 1   MQATTHPP----ATSARSKVSAIFRVTSGNFLEQFDFFLFGFYATYIAAAFFPASSEFAS 56

Query: 68  LMMTFAVFGAGFLMRPIGAIVLGAYIDKVGRRKGLIVTLSIMATGTFLIVLIPSYQTIGL 127
           LMMTFAVFGAGFLMRP+GA++LGAYID VGRRKGLIVTLSIMA+GT LIVL+P Y+TIGL
Sbjct: 57  LMMTFAVFGAGFLMRPLGAVILGAYIDDVGRRKGLIVTLSIMASGTILIVLVPGYETIGL 116

Query: 128 WAPLLVLIGRLLQGFSAGAELGGVSVYLAEIATPGRKGFYTSWQSGSQQVAIMVAAAMGF 187
           +AP LVLIGRLLQGFSAGAELGGVSVYLAEIATPGRKGF+TSWQS SQQVAI+VAAA+G+
Sbjct: 117 FAPALVLIGRLLQGFSAGAELGGVSVYLAEIATPGRKGFFTSWQSASQQVAIVVAAALGY 176

Query: 188 ALNAVLEPSAISDWGWRIPFLFGVLIVPFIFILRRKLEETQEFTARRHHLAMRQVFATLL 247
           ALN  +  + ++DWGWRIPF  G +IVPFIF+LRR LEET EFTARRH  +MRQVF TLL
Sbjct: 177 ALNQWMPATVVADWGWRIPFFVGCMIVPFIFLLRRSLEETAEFTARRHRPSMRQVFGTLL 236

Query: 248 ANWQVVIAGMMMVAMTTTAFYLITVYAPTFGKKVLMLSASDSLLVTLLVAISNFFWLPVG 307
            NWQ+VIAGM+MVA+TTTAFYLITVYAPTFGK VL LS SD+LLVTLLV +SNF WLP+G
Sbjct: 237 QNWQIVIAGMLMVALTTTAFYLITVYAPTFGKTVLHLSTSDALLVTLLVGVSNFCWLPLG 296

Query: 308 GALSDRFGRRSVLIAMTLLALATAWPALTMLANAPSFLMMLSVLLWLSFIYGMYNGAMIP 367
           GALSDR GRR VL+AMTLL LATA+PALT L  APSF+ ML VLLWLSFIYG+YNGAM+ 
Sbjct: 297 GALSDRIGRRPVLVAMTLLTLATAYPALTYLVQAPSFINMLLVLLWLSFIYGLYNGAMVA 356

Query: 368 ALTEIMPAEVRVAGFSLAYSLATAVFGGFTPVISTALIEYTGDKASPGYWMSFAAICGLL 427
           ALTEIMP EVRVAGFSLAYSLATAVFGGFTP IST LI+Y+GDKA+PGYWMSFAA+C L 
Sbjct: 357 ALTEIMPVEVRVAGFSLAYSLATAVFGGFTPAISTFLIQYSGDKAAPGYWMSFAALCALC 416

Query: 428 ATCYLYRRSAVALQTA 443
           AT YLYRRS   LQ A
Sbjct: 417 ATLYLYRRSTGRLQVA 432


Lambda     K      H
   0.329    0.139    0.421 

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: 738
Number of extensions: 19
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: 444
Length of database: 434
Length adjustment: 32
Effective length of query: 412
Effective length of database: 402
Effective search space:   165624
Effective search space used:   165624
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 (21.9 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