GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12650 in Acidovorax sp. GW101-3H11

Align D-lactate transporter, permease component 1 (characterized)
to candidate Ac3H11_1431 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= reanno::Phaeo:GFF1249
         (400 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1431
          Length = 333

 Score =  179 bits (455), Expect = 8e-50
 Identities = 118/362 (32%), Positives = 178/362 (49%), Gaps = 57/362 (15%)

Query: 32  GSALAQFNAGYPDLMQRFVIFGIFAIGFNILFGLTGYLSFGHAAFLGVGSYSAVWMFKLL 91
           G  +A F   YP  + + + F +FA  FN+L G TG LSFGHAAFLG  +Y A    K+ 
Sbjct: 17  GLVVAPFLGAYPVFVMKLMCFALFASAFNLLLGFTGLLSFGHAAFLGGAAYVAGHAIKVW 76

Query: 92  SMNVVPAIVLSVIVAGLFALVIGYVSLRRSGIYFSILTLAFAQMSFNLAYSVLTPITNGE 151
            +     ++L      L  L+ G++++RR GIYFS++TLA AQM F          T GE
Sbjct: 77  GLTPEVGLLLGTAGGALLGLLFGWLAIRRQGIYFSMITLALAQMLFFACLQA--KFTGGE 134

Query: 152 TGLQLTLDDPRVLGVSATADGSIPVTSLFG-LEMRSTFEMVVGPWAFQFNAGYYLCALIL 210
            GLQ                  +P   LFG ++++S   M            YY+  +I+
Sbjct: 135 DGLQ-----------------GVPRGKLFGVIDLQSDLVM------------YYVALVIV 165

Query: 211 LAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNTRPYTLAAFVISGMYAGLAGGLMAS 270
             AF L +R   SPFG +LK +K N+ R    G +T  + L AFV+S   AGLAG L   
Sbjct: 166 ALAFLLIVRTIHSPFGQVLKGIKENEPRAISLGYDTHRFKLLAFVLSAALAGLAGSLKTL 225

Query: 271 MDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVLGAGFIKYFENIFSKINDNVLHS--- 327
           +   A    + WTASG+V+LMT++GG GTL GP++G+  +   EN   +   N+L +   
Sbjct: 226 VLGFATLSDVHWTASGQVILMTLVGGLGTLSGPLIGSAVVVLLENKIGEFG-NLLAALTS 284

Query: 328 --WFSFMPDGIEDAMVFIVHPFIGKGWHLTLGILFMLVVIFLPGGLVEGGQKLRGWIQGR 385
             WF                  +G+   +  G++F++ V+    G++    ++  W+  R
Sbjct: 285 VEWFK----------------TLGESVTMVTGLIFVICVLAFRRGIM---GEIIAWLAQR 325

Query: 386 KA 387
           +A
Sbjct: 326 RA 327


Lambda     K      H
   0.327    0.143    0.435 

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: 463
Number of extensions: 31
Number of successful extensions: 2
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: 400
Length of database: 333
Length adjustment: 30
Effective length of query: 370
Effective length of database: 303
Effective search space:   112110
Effective search space used:   112110
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 (21.7 bits)
S2: 49 (23.5 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