Alignments for a candidate for Shew_2731 in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for Shew_2731 in Hydrogenophaga taeniospiralis NBRC 102512

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate WP_068166469.1 HTA01S_RS00855 cation acetate symporter

Query= reanno::PV4:5209923
         (572 letters)



>NCBI__GCF_001592305.1:WP_068166469.1
          Length = 600

 Score =  716 bits (1849), Expect = 0.0
 Identities = 372/606 (61%), Positives = 456/606 (75%), Gaps = 40/606 (6%)

Query: 1   MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60
           MD+QT TYL VG +FALY+GIA W+RAGS  EFYVAGGGVHP+ NGMATAADWMSAASFI
Sbjct: 1   MDLQTTTYLFVGASFALYLGIAFWARAGSVSEFYVAGGGVHPITNGMATAADWMSAASFI 60

Query: 61  SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120
           S+AG++S +GY G+V+LMGWTGGYVLLA+ +APYLRKFGKFTVP FIGDR+YS+ A TVA
Sbjct: 61  SMAGLISNMGYGGAVFLMGWTGGYVLLAMLLAPYLRKFGKFTVPQFIGDRFYSKTASTVA 120

Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180
           V+C +    TYI GQM GVGV FSRFL V  DTG+YIG A+VFFYAV GGMKGITYTQVA
Sbjct: 121 VICLLTASTTYIIGQMTGVGVAFSRFLNVSSDTGIYIGQAIVFFYAVFGGMKGITYTQVA 180

Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFS 240
           QY VLIFA+++PAIFIS+ +TG  LPQLG GA+L   AG +T   LL KLD +   LGF+
Sbjct: 181 QYIVLIFAYIIPAIFISLNLTGSFLPQLGLGADL---AGTDTA--LLAKLDQVVTDLGFN 235

Query: 241 QYTEGSKG-MIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTT 299
           QYT  S G M+++FF T +LM GTAGLPHVIVRFFTVPKV DAR SAGWALVFIA++YTT
Sbjct: 236 QYTTTSAGSMLNMFFYTVSLMIGTAGLPHVIVRFFTVPKVADARASAGWALVFIALLYTT 295

Query: 300 IPALAAFSRVNMIETIN-GPESTGVAY--------ETAPDWIKNWEKTGLIKWDDKNNDG 350
            PA+ A +++N+  T+N    S G  Y        E  PDW+K WEKTGL+KW+DKN DG
Sbjct: 296 APAVGAMAKLNLHSTVNTAVMSNGDLYATESSLKNEDRPDWMKRWEKTGLLKWEDKNADG 355

Query: 351 KIYYAKGET----------------NEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAA 394
           +I Y    T                NE+ ++ DI+VLA PEIA LP WVIALVAAGG+AA
Sbjct: 356 RIQYYNDATKNEIAKSKATAAGWKGNELTVNADIIVLANPEIALLPNWVIALVAAGGIAA 415

Query: 395 ALSTSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAAALGIVMAGYFGINPPGFV 454
           ALST+AGLL+ IS++VSHDL+K  F P+IS+K ELL  +IA A+ IV+AG+ G+NPPGF 
Sbjct: 416 ALSTAAGLLMAISSAVSHDLIKNVFNPNISEKGELLAGKIAMAVAIVLAGWLGLNPPGFA 475

Query: 455 AAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFK---FVNPG 511
           A  VA+AFG+AASS+FPAI+MGIFSRTM+ +GAIAGM+ GLL +  Y+   K   F+   
Sbjct: 476 AGTVALAFGIAASSIFPAIMMGIFSRTMSDKGAIAGMLSGLLVTLFYVFAHKGLFFIKGT 535

Query: 512 D-----NNASNWLFGISPEGIGMLGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGA 566
           D        + W FGI+PE +G +G I+NF VAF+V+K+TA  P+++ ++VESIR PKGA
Sbjct: 536 DFVDMVGGVNGW-FGITPEAVGTVGAIVNFTVAFLVNKLTAPAPKHIQELVESIRVPKGA 594

Query: 567 GEAHDH 572
           G A  H
Sbjct: 595 GAATGH 600


Lambda     K      H
   0.326    0.140    0.423 

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: 1095
Number of extensions: 50
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: 572
Length of database: 600
Length adjustment: 37
Effective length of query: 535
Effective length of database: 563
Effective search space:   301205
Effective search space used:   301205
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 24 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:

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