Alignments for a candidate for actP in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Dinoroseobacter shibae DFL-12

Align actP-like component of D-alanine uptake system (characterized)
to candidate 3610175 Dshi_3556 Na+/solute symporter (RefSeq)

Query= reanno::psRCH2:GFF346
         (589 letters)



>FitnessBrowser__Dino:3610175
          Length = 598

 Score =  828 bits (2140), Expect = 0.0
 Identities = 427/599 (71%), Positives = 486/599 (81%), Gaps = 11/599 (1%)

Query: 1   MSQYWINMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFI 60
           M Q  +N++ VG SF LY GIA+WARAGST EFY AG GV+PV NGMATAADWMSAASFI
Sbjct: 1   MDQTTLNIIVVGLSFALYFGIAIWARAGSTSEFYAAGRGVNPVVNGMATAADWMSAASFI 60

Query: 61  SMAGLIASGGYATSVYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYSRGARLTA 120
           SMAGLIA  GY+ S +LMGWTGGYVL+A+LLAPYLRKFGKFTVP+FIGDRFYS  AR+  
Sbjct: 61  SMAGLIAFVGYSNSSFLMGWTGGYVLMALLLAPYLRKFGKFTVPEFIGDRFYSTKARVVG 120

Query: 121 VVCLILISVTYVIGQMAGAGVAFSRFLEVSNSAGIWIAAAIVFAYAVFGGMKGITYTQVA 180
           V+CLI+IS TYVIGQM GAGVAFSRFLEVS++ G+  A+ +VF YAV GGMKGITYTQVA
Sbjct: 121 VICLIVISTTYVIGQMTGAGVAFSRFLEVSSTTGLVTASCVVFVYAVLGGMKGITYTQVA 180

Query: 181 QYIVLIIAYTIPAVFIAMQLTGNPIPMFGMFGT----HVDSGVPLLDKLDQVVTDLGFAA 236
           QY+VLIIAYTIPA+FI++QLTGNPIP  G+F       V +G PLL  LD ++TDLGF A
Sbjct: 181 QYVVLIIAYTIPAIFISLQLTGNPIPGLGLFSNMAPGQVGAGEPLLVTLDGLLTDLGFNA 240

Query: 237 YTADVDNKLNMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYLTAP 296
           YT    +   M LFTLSLMIGTAGLPHVIIRFFTVP+VADAR SAGWTLVFIALLYLTAP
Sbjct: 241 YTTG-SSPFLMALFTLSLMIGTAGLPHVIIRFFTVPRVADARISAGWTLVFIALLYLTAP 299

Query: 297 AVASMARLNLVNTIYPEGPQAEAIRYE---DRPE--WVQTWERTGLIKWEDKNADGRVQM 351
           AV +MARLN+ + ++PEG Q EA+  E   + PE  W+ TW++TGL+ WEDKN DGR+Q 
Sbjct: 300 AVGAMARLNITDLMWPEGTQGEAVTIEMIQNDPEYAWMNTWQQTGLLGWEDKNGDGRIQY 359

Query: 352 YNDANAKFTPTATERGWNGNELT-VNNDIIVLANPEIANLPGWVIGLIAAGAIAAALSTA 410
           YNDAN   T  A   GW GNELT  N DI+VLANPEIANLPGWVI LIAAG IAAALSTA
Sbjct: 360 YNDANPSMTERAEAAGWQGNELTNFNRDILVLANPEIANLPGWVIALIAAGGIAAALSTA 419

Query: 411 AGLLLAISSAISHDLIKTLINPKISEKNEMLAARLSMTAAILLATWLGLNPPGFAAQVVA 470
           AGLLLAISSAISHDLIKT+ NP ISEK E+LAAR+SM  AI++AT+LGLNPPGFAAQVVA
Sbjct: 420 AGLLLAISSAISHDLIKTVFNPSISEKGELLAARISMAGAIVVATYLGLNPPGFAAQVVA 479

Query: 471 LAFGLAAASLFPALMMGIFSKRVNSKGAVAGMLVGVISTAVYIFLYLGWFFIPGTASIPN 530
           LAFGLAAA+LFPALMMGIFSKR+N+ GA  GMLVG+IST  Y+F YLG FF+PGT  +  
Sbjct: 480 LAFGLAAATLFPALMMGIFSKRINASGATWGMLVGLISTCAYLFTYLGIFFVPGTNFLEP 539

Query: 531 TPDQWWMGISPQAFGAVGAMLNFAVAYAVSMATEAPPQEIQDLVESVRTPKGAGVALDH 589
           T   +  GI P  FG +GA+LNFAVA  VS ATE PPQEIQDLVESVR P+GAG A+DH
Sbjct: 540 TASNYLFGIPPTHFGPIGALLNFAVAILVSRATEEPPQEIQDLVESVRIPRGAGAAVDH 598


Lambda     K      H
   0.324    0.137    0.419 

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: 1140
Number of extensions: 48
Number of successful extensions: 5
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: 589
Length of database: 598
Length adjustment: 37
Effective length of query: 552
Effective length of database: 561
Effective search space:   309672
Effective search space used:   309672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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
the source code
instructions for running GapMind on your computer

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