GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tctA in Acidovorax sp. GW101-3H11

Align Citrate uptake transporter, membrane subunit, component of Pmf-dependent citrate uptake porter, TctABC (characterized)
to candidate Ac3H11_61 Tricarboxylate transport membrane protein TctA

Query= TCDB::S5Y5N9
         (510 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_61 Tricarboxylate
           transport membrane protein TctA
          Length = 494

 Score =  468 bits (1204), Expect = e-136
 Identities = 231/496 (46%), Positives = 331/496 (66%), Gaps = 7/496 (1%)

Query: 8   MEGFAGALTPMNLLWVIVGCLLGTAVGVMPGLGSSMAVALLLPMTFALDPTAAFIMFSGV 67
           M+GFA A TP+NLLW  VGC++GTAVGV+PG+G ++AVA+LLP+T  ++ TA+ I F+G+
Sbjct: 1   MQGFATAATPINLLWAFVGCMIGTAVGVLPGIGPAVAVAMLLPITVKVEATASMIFFAGI 60

Query: 68  YFGGLFGDSTMAILMNTPGQASAIASTFEGHRMALNGRAPQALATAAIGAFIGGIVSSFI 127
           Y+G ++G ST +IL+NTPG+A ++ +  EG++MA NGRA  ALATAAIG+F+ G +++ +
Sbjct: 61  YYGAMYGGSTTSILLNTPGEAGSMVTAMEGNKMAKNGRAGAALATAAIGSFVAGTIATVL 120

Query: 128 VVFLAPTLAELSTAFGPAEYFALALFAFVATSSVVSDSVFKGLASLIFGLGIATIGIDSV 187
           V F AP +AE +   GP EYF L + AF   S+V+  S  +G+ +L  GL +  IGID +
Sbjct: 121 VTFFAPLVAEYAVRLGPPEYFMLMVLAFTTVSAVLGKSTLRGMVALFVGLAMGLIGIDQL 180

Query: 188 TGIERFTLGAPQLFDGISLVTVTVAILALGEVFY-IAARARRDKANLETRSAGRPWLTGT 246
           TG  R+T G P+L DGI +V + V + A+GE  Y +    + D+      S     +T  
Sbjct: 181 TGQARYTGGVPELMDGIEVVLIAVGLFAVGEALYNVMYEGKTDETQNRLTST---HMTKE 237

Query: 247 EFKEAAPAWARGTIIGLPFGVIPVGGSEVPTFLAYSTERALDKRRKDPQFGDKGAIRGLA 306
           E+K + PAW R T IG PFG +P GGSE+PTFL+Y+ E+ L K ++  +FG  GAI G+A
Sbjct: 238 EWKRSWPAWLRATFIGFPFGTVPAGGSEIPTFLSYAAEKKLSKNKE--EFGTTGAIEGVA 295

Query: 307 APEAAGNATTGMAMGALLALGLPVSATAAIMLAAFRQYGIQPGPLLFDRNPELVWALLAS 366
            PEAA NA     +  LL LG+P S T AI+L AF+ YGIQPGP LFD N  LVWAL+AS
Sbjct: 296 GPEAANNAAITATLIPLLTLGIPTSNTTAILLGAFQNYGIQPGPQLFDTNGALVWALIAS 355

Query: 367 FFIAMIVLLFINLPFAQLWAKLLLIPNHYLYSGIALFCGLGIYATSGAVFDLLMLLGIGV 426
            +I  ++LL +NLP   LW KLL IP  YLY+GI +F  LG+Y    + FDL++L  IG+
Sbjct: 356 MYIGNVMLLILNLPLVGLWVKLLNIPKSYLYAGILVFSTLGVYGMRQSAFDLVLLYAIGL 415

Query: 427 VALIMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDFSILVSSPITWSLYA-VLAIF 485
           + ++MRR+ +P AP+++GM+LGPLAE  +R+A+    G ++I +  P + +L   VLA+ 
Sbjct: 416 LGVVMRRFDFPAAPVVVGMILGPLAEAQMRNAVAIGEGKWTIFLERPGSVTLIVIVLAVL 475

Query: 486 IAVSVITAIRGRRKHL 501
           I   ++     R+  L
Sbjct: 476 IVPRLLRRWAARKMAL 491


Lambda     K      H
   0.326    0.141    0.414 

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: 751
Number of extensions: 38
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 510
Length of database: 494
Length adjustment: 34
Effective length of query: 476
Effective length of database: 460
Effective search space:   218960
Effective search space used:   218960
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 (21.6 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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