GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_61
          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:

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