GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Azospirillum thiophilum BV-S

Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_045584776.1 AL072_RS30790 TRAP transporter large permease subunit

Query= uniprot:I7DRS6
         (467 letters)



>NCBI__GCF_001305595.1:WP_045584776.1
          Length = 427

 Score =  259 bits (661), Expect = 2e-73
 Identities = 151/454 (33%), Positives = 246/454 (54%), Gaps = 37/454 (8%)

Query: 6   LFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIPFFIL 65
           + ++++ LL+ G+PI  ALGL+S   L ++ + S+ S+A ++F +      L  IP F  
Sbjct: 5   ILALLLVLLMSGMPIFAALGLTSLGVLALF-EGSIDSMADSVFASLNNPL-LATIPMFAF 62

Query: 66  ASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIVIA 125
            +  M    V   +   S   VGH+ GGL+ A + +C +F+ +SGSS AT + IGSI I 
Sbjct: 63  MAHVMIKAKVVDDLYEMSNTLVGHIKGGLSFATILSCTIFSTISGSSVATALTIGSISIP 122

Query: 126 GMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMAGLM 185
            M++ GY +    G+I   GTLGILIPPS  M++YA   + S+G +FLAG+IPGL+  ++
Sbjct: 123 QMKRYGYRQRDTYGLIAAGGTLGILIPPSGPMILYAIVTDASIGALFLAGIIPGLLMAVV 182

Query: 186 LMVTIYVMAKVKNLPKGE-WLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTEAAAV 244
                ++ AK ++  + + W G+G VAA+   +   +L+  +ILGGIY G+FT  EAAAV
Sbjct: 183 FAGYSWLQAKRQDGVRSQSWPGFGAVAAAFRKSIWAVLMPPLILGGIYLGVFTAGEAAAV 242

Query: 245 ASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTRHALF 304
            +VYA  VA  VYR++                                    AD      
Sbjct: 243 GAVYALAVALLVYRNLSV----------------------------------ADLLDCGV 268

Query: 305 EAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIGGQF 364
           +  + +  L  +IA A +  H +T  ++P QI   + + G     F++ V   + I G F
Sbjct: 269 QTMRTSAMLFMIIAAAGMFGHAITIIRLPAQIMETVTALGLSQGGFILAVMAAIFILGMF 328

Query: 365 MEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVAGMPM 424
           +E   +++I  P++ P+   LGI+P+  G+++++N+E+ +ITPPVG+NLFV  G+    +
Sbjct: 329 LETIAIILITTPIILPVMAALGINPVWYGVMLMINLELALITPPVGMNLFVIKGITNSSL 388

Query: 425 MAVVRAALPFLAVLFVFLIMITYIPWISTVLPNA 458
             V R ALP++ ++   L ++   P +S  LP A
Sbjct: 389 GEVTRGALPYVLLMMAGLFIVWLFPALSLWLPQA 422


Lambda     K      H
   0.329    0.144    0.421 

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: 588
Number of extensions: 39
Number of successful extensions: 4
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: 467
Length of database: 427
Length adjustment: 33
Effective length of query: 434
Effective length of database: 394
Effective search space:   170996
Effective search space used:   170996
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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