GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ectP in Dietzia timorensis ID05-A0528

Align Ectoine/glycine betaine/proline transporter EctP (characterized)
to candidate WP_067477459.1 BJL86_RS14655 BCCT family transporter

Query= SwissProt::Q79VE0
         (615 letters)



>NCBI__GCF_001659785.1:WP_067477459.1
          Length = 632

 Score =  303 bits (775), Expect = 2e-86
 Identities = 180/541 (33%), Positives = 289/541 (53%), Gaps = 25/541 (4%)

Query: 25  IFSISVGFIVVFVIATIALGEKARTTFSAIAGWLLENLGWMYIGGVSLVFIFLMGIFA-S 83
           +F+ +   IV F+   I   +   T  S + GW +ENLGW+ +  V ++ + +M   A S
Sbjct: 43  LFATTAALIVAFIAWGIIDPDSVGTVSSTMFGWAIENLGWL-LNIVMILGLAVMTYLAFS 101

Query: 84  RYGRVKLGDDDDDPEHTLIVWFCMLFAGGVGAVLMFWGVAEPINHAFNVPMANEESMSEA 143
           R+GR+KLG DD++PE  L  W  M+F  G+G  + F+G +EP++H    P  + +  +  
Sbjct: 102 RFGRIKLGKDDEEPEFALFSWVAMMFGAGIGVGIFFFGPSEPLSHYLTPPPHSVDPETPE 161

Query: 144 AIVQAFAYTFYHFGIHMWVIMALPGLSLGYFIYKRKLPPRLSSVFSPILGK-HIYSTPGK 202
           A+  + A + +H+G+ +W + A+ G +L Y  Y+R     LSSVF  ++G        G 
Sbjct: 162 ALHLSMAQSHFHWGLMIWALYAMVGGALAYSSYRRGRVTLLSSVFKSLIGSDRSEGLAGS 221

Query: 203 LIDVLAIVGTTFGIAVSVGLGVLQINAGMNKLWSTPQVSWVQLLIIL-IITAVACISVAS 261
           +ID++AI+ T FG A ++GL  +QI  G+  +    +V+   L++I+ I+TA   +S  S
Sbjct: 222 IIDMMAIIATLFGTAATLGLSAIQIGQGVQIVSGVSEVTNTVLIVIIGILTACFIVSAVS 281

Query: 262 GLDKGIKLLSNINIAMAVALMFFILFTGPTLTLLRFLVESFGIYASWMPNLMFWTDSF-Q 320
           G+ +GI+ LSN+NI + + L+ F+   GPTL LL  +      YA  + ++M    S+ Q
Sbjct: 282 GVSRGIRYLSNLNITLTLGLILFVFLLGPTLFLLNLVPAGILSYADNLLDMMSRGLSWGQ 341

Query: 321 DNPGWQGKWTVFYWAWTICWSPYVGMFVARISRGRTVREFIGGVLALPAIFGVVWFSIFG 380
           D   +Q  WT FYWAW I W+P+VGMF+ARISRGRT+R+F       P    ++ F+IFG
Sbjct: 342 DTIEFQAVWTSFYWAWWIAWTPFVGMFIARISRGRTIRQFALVTTLAPTFILILAFTIFG 401

Query: 381 RAGIEVELSN-PGFLTQPTVVEGDVPA--ALFNVLQEYPLTGIVSAFALVIIVIFFITSI 437
              I     + PGF       +G   +   LF++    PL  +     + ++ +FFITS 
Sbjct: 402 GTAISFSREDFPGF-------DGSASSENVLFSLFDNLPLGTVTPLIIIFVLAVFFITSA 454

Query: 438 DSAALVNDMFATGAENQTPTSYR---VMWACTIGAVAGSLLIISPSSGIATLQEVVIIVA 494
           DSA++V     T +E   P   +   V W   +  +A  +L++   + +  LQ + I++A
Sbjct: 455 DSASVV---MGTLSEKGNPAPNKLIVVFWGLCMMGIAVVMLLVGGETALTGLQNLTILIA 511

Query: 495 FPFFLVQFVMMFSLLKGMSEDAAAVRRVQTRQWEKTDTPEKLEEHSS----QPAPGYDDE 550
            PF +V   +  + LK +S D AA+RR   +   K    + LEEH        AP  D  
Sbjct: 512 IPFSVVLVGLAVAFLKDLSTDPAAIRRTYAQTAIKNAVVKGLEEHGDDFEISVAPSTDGR 571

Query: 551 G 551
           G
Sbjct: 572 G 572


Lambda     K      H
   0.324    0.140    0.434 

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: 1058
Number of extensions: 50
Number of successful extensions: 7
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: 615
Length of database: 632
Length adjustment: 37
Effective length of query: 578
Effective length of database: 595
Effective search space:   343910
Effective search space used:   343910
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: 54 (25.4 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