GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Phaeobacter inhibens BS107

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC

Query= TCDB::Q52665
         (434 letters)



>FitnessBrowser__Phaeo:GFF196
          Length = 432

 Score =  411 bits (1057), Expect = e-119
 Identities = 225/441 (51%), Positives = 288/441 (65%), Gaps = 18/441 (4%)

Query: 1   MSDT-----SFVRTEMLAPRPAPVSQVGAIKWMRENLFSGPLNTALTVFGLLATVWLVQA 55
           MSDT     +FVR   + P P P  + G  KW+RENLFS   N+ LT+  L     L+ +
Sbjct: 1   MSDTHAQTVAFVRETQIPPAPPPGRETGVYKWIRENLFSSVPNSILTLAALALIYALLSS 60

Query: 56  AAPWLLHGVWNANSLTECRAIIAERWGPEATGACWAVIRVRWNQFLFGF-YPVDQYWRLF 114
             PWLL+GVW  NSL ECR ++  +      GAC++V+  RWNQ L+GF YP  +YWR  
Sbjct: 61  TLPWLLNGVWTTNSLAECREVLDGK-----LGACFSVLTERWNQLLYGFKYPGTEYWRPN 115

Query: 115 VTFAGLFLALAPVLFDALPRKLIWGTLLYPLAAFWLLWGGPIWGPVSVLAGFAILGLLFT 174
           +    L +ALAPVLF  LPRKL+  T +YP  AFWL+WGG I  P+  L GF   G +F 
Sbjct: 116 LALVLLLVALAPVLFFDLPRKLLAFTAIYPFLAFWLIWGGSILVPIVALLGFVAAGFVFQ 175

Query: 175 ALAPKLGVPVSAGIGLVVAALF-WLYAAAPI-EAALQSALPLALPEVDSDQFGGFLLALV 232
                 G       G +VAA+  W      I E A  +A+  A+P  D    GGF+L ++
Sbjct: 176 KFGK--GSFALGFFGAIVAAVVVWNIGGFLIPEGASDNAMLSAVPSRD---LGGFMLNMM 230

Query: 233 IGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPP 292
           +GVT + +S+PLGI LALGRQS+M ++K + V  IEFVRGVPLITLLF AS++L YF PP
Sbjct: 231 LGVTCVSLSVPLGIALALGRQSNMPLIKWICVVFIEFVRGVPLITLLFVASVMLSYFFPP 290

Query: 293 GTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQA 352
               DL LRVVI++TLF+AAYIAEVIRGGLAALP+GQYEAAD+LGLDY QA RLII+PQA
Sbjct: 291 DATVDLFLRVVIMITLFSAAYIAEVIRGGLAALPKGQYEAADSLGLDYPQAMRLIILPQA 350

Query: 353 LKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEPYIFVALIFF 412
           LKISIPGIV+  +GLFKDTTLV+ + +FD +  I   + +   W G YWE   F A +FF
Sbjct: 351 LKISIPGIVNVAVGLFKDTTLVSVISMFDLVGMIRGPILASTEWNGVYWELLGFAAFLFF 410

Query: 413 LFNFSMSRYSMYLERKLKRDH 433
           +  + +S+YS +LER+L  DH
Sbjct: 411 IVCYGISQYSQWLERRLATDH 431


Lambda     K      H
   0.329    0.143    0.457 

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: 688
Number of extensions: 34
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: 434
Length of database: 432
Length adjustment: 32
Effective length of query: 402
Effective length of database: 400
Effective search space:   160800
Effective search space used:   160800
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 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