Alignments for a candidate for ectP in Algiphilus aromaticivorans DG1253

GapMind for catabolism of small carbon sources

Alignments for a candidate for ectP in Algiphilus aromaticivorans DG1253

Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate WP_052367903.1 U743_RS10350 BCCT family transporter

Query= SwissProt::Q87NZ5
         (553 letters)



>NCBI__GCF_000733765.1:WP_052367903.1
          Length = 538

 Score =  642 bits (1657), Expect = 0.0
 Identities = 316/526 (60%), Positives = 388/526 (73%), Gaps = 23/526 (4%)

Query: 20  DTDYQIGQDNVALKVGPFGLDIHNRVFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLV 79
           D DY+IGQDN+ +    FGLDIHN VF +SG  IV FV+  L F    E     LR W+ 
Sbjct: 14  DFDYEIGQDNIQI----FGLDIHNPVFIVSGGLIVAFVIYALGFSAHAEATLGELRPWIT 69

Query: 80  SNLDWFFLASGNVFVIVCLVLIVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVF 139
           S  DW  + + N+FV+ CL L+V+P G++R+GG EATPDY YAGW AMLFAAGMGIGL+F
Sbjct: 70  STFDWVLMGAANIFVLFCLFLLVSPWGKIRLGGPEATPDYGYAGWFAMLFAAGMGIGLMF 129

Query: 140 FGVSEPMSHFSSALGGVNIENGVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIY 199
           FGV EPM HF +   GV  EN                 AA+A GMAATI+HW LHPW+IY
Sbjct: 130 FGVLEPMYHFENPPLGVGKENAA---------------AAAAAGMAATIFHWGLHPWAIY 174

Query: 200 ALLALGLAIFSFNKGLPLTMRSIFYPLFGERVWGWVGHIIDILAVVATVFGLATSLGYGA 259
           A++AL LA F+FN+G+PLT+RS F+P+ G+RVWGW GH+IDILAV AT+FGLATSLG+GA
Sbjct: 175 AVVALSLAFFTFNRGMPLTIRSGFHPILGDRVWGWPGHLIDILAVFATMFGLATSLGFGA 234

Query: 260 SQAATGLNFLFGVPMTDTTQVVLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFF 319
            QA  GL++LF  P    TQV L++ IT++ALISV+ GLD GVKRLSE+NM+LA +LL F
Sbjct: 235 QQAGAGLHYLFNTPEGIPTQVGLVIGITSVALISVLRGLDGGVKRLSELNMMLALLLLLF 294

Query: 320 VIIVGPTMAILTGFFDNIASYITNIPALSMPFEREDVNYSQGWTAFYWAWWISWSPFVGM 379
           VI VG  + I+TGFF     Y  ++  LS P  RED+++  GWT FYWAWWISWSPFVGM
Sbjct: 295 VIAVGGVVDIITGFFGAAYYYARDVLPLSNPVGREDLDFMHGWTTFYWAWWISWSPFVGM 354

Query: 380 FIARVSRGRSVREFIICVILIPSTVCVLWMTAFGGTAISQYVNDGYEAVFNAEL----PL 435
           FIARVSRGR+VREFI CV++IP+TV VLWMTAFGGTA+ QY+N GY+ V          L
Sbjct: 355 FIARVSRGRTVREFITCVLVIPTTVSVLWMTAFGGTAVRQYLNTGYDGVMKTVTDYTPEL 414

Query: 436 KLFAMLDVMPFAEITSVVGIILVVVFFITSSDSGSLVIDTIAAGGKVDAPTPQRVFWCTF 495
            LFAML+ +PF  +TS +GI+LV+VFF+TSSDSGSLVIDTI AGGK+DAP  QRVFWC F
Sbjct: 415 SLFAMLEALPFTAVTSFIGIVLVIVFFVTSSDSGSLVIDTITAGGKLDAPVAQRVFWCLF 474

Query: 496 EGLVAIALMLGGGLAAAQAMAVTTGLPFTIVLLVATVSLIKGLMDE 541
           EGLVAIAL++GGGLA+ QA A+TTGLPF +VL++ T  +  GL  E
Sbjct: 475 EGLVAIALLVGGGLASLQAAAITTGLPFAVVLVILTFCVALGLRKE 520


Lambda     K      H
   0.327    0.141    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: 1007
Number of extensions: 54
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: 553
Length of database: 538
Length adjustment: 35
Effective length of query: 518
Effective length of database: 503
Effective search space:   260554
Effective search space used:   260554
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources