Alignments for a candidate for actP in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Shewanella loihica PV-4

Align actP-like component of D-alanine uptake system (characterized)
to candidate 5209923 Shew_2371 Na+/solute symporter (RefSeq)

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



>FitnessBrowser__PV4:5209923
          Length = 572

 Score =  676 bits (1743), Expect = 0.0
 Identities = 338/589 (57%), Positives = 430/589 (73%), Gaps = 27/589 (4%)

Query: 6   INMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFISMAGL 65
           +  L VG +F LYIGIA+W+RAGSTKEFYVAGGGVHPV NGMATAADWMSAASFIS+AG+
Sbjct: 6   LTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGI 65

Query: 66  IASGGYATSVYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYSRGARLTAVVCLI 125
           ++  GY  SVYLMGWTGGYVLLA+ +APYLRKFGKFTVPDFIGDR+YS+ AR  AVVC I
Sbjct: 66  VSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAI 125

Query: 126 LISVTYVIGQMAGAGVAFSRFLEVSNSAGIWIAAAIVFAYAVFGGMKGITYTQVAQYIVL 185
            I  TY+ GQM G GV FSRFLEV    G++I  A+VF YAV GGMKGITYTQVAQY VL
Sbjct: 126 FICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVL 185

Query: 186 IIAYTIPAVFIAMQLTGNPIPMFGMFGTHVD-----SGVPLLDKLDQVVTDLGFAAYTAD 240
           I A+ +PA+FI++ +TG+ +P  G     VD     +GV LL+KLD +   LGF+ YT  
Sbjct: 186 IFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFSQYTEG 245

Query: 241 VDNKLNMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYLTAPAVAS 300
               +++F  T +LM GTAGLPHVI+RFFTVPKV DAR SAGW LVFIA++Y T PA+A+
Sbjct: 246 SKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAA 305

Query: 301 MARLNLVNTIYPEGPQAEAIRYEDRPEWVQTWERTGLIKWEDKNADGRVQMYNDANAKFT 360
            +R+N++ TI   GP++  + YE  P+W++ WE+TGLIKW+DKN DG++           
Sbjct: 306 FSRVNMIETI--NGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGET---- 359

Query: 361 PTATERGWNGNELTVNNDIIVLANPEIANLPGWVIGLIAAGAIAAALSTAAGLLLAISSA 420
                     NE+ ++ DI+VLA PEIANLP WVI L+AAG +AAALST+AGLLL IS++
Sbjct: 360 ----------NEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTS 409

Query: 421 ISHDLIKTLINPKISEKNEMLAARLSMTAAILLATWLGLNPPGFAAQVVALAFGLAAASL 480
           +SHDL+K    P IS+K E+L AR++    I++A + G+NPPGF A VVA+AFGLAA+SL
Sbjct: 410 VSHDLLKKNFMPDISDKQELLYARIAAALGIVMAGYFGINPPGFVAAVVAIAFGLAASSL 469

Query: 481 FPALMMGIFSKRVNSKGAVAGMLVGVISTAVYIFLYLGWFFIPGTASIPNTPDQWWMGIS 540
           FPA++MGIFS+ +N +GA+AGM++G++ +A YI  +   F  PG     N    W  GIS
Sbjct: 470 FPAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFK--FVNPG----DNNASNWLFGIS 523

Query: 541 PQAFGAVGAMLNFAVAYAVSMATEAPPQEIQDLVESVRTPKGAGVALDH 589
           P+  G +G ++NFAVA+ VS  T A PQ + D+VES+R PKGAG A DH
Sbjct: 524 PEGIGMLGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEAHDH 572


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: 1033
Number of extensions: 47
Number of successful extensions: 6
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: 572
Length adjustment: 36
Effective length of query: 553
Effective length of database: 536
Effective search space:   296408
Effective search space used:   296408
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, 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