GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Burkholderia phytofirmans PsJN

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate BPHYT_RS17470 BPHYT_RS17470 glycerol-3-phosphate ABC transporter ATP-binding protein

Query= reanno::psRCH2:GFF857
         (371 letters)



>FitnessBrowser__BFirm:BPHYT_RS17470
          Length = 362

 Score =  333 bits (854), Expect = 4e-96
 Identities = 187/361 (51%), Positives = 242/361 (67%), Gaps = 16/361 (4%)

Query: 1   MASVTLRDICKSYDGTPITRH-IDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGD 59
           MA++TL+ + K+YDG     H ID+D+ DGEFVV VGPSGCGKSTLLR++AGLE I+ G 
Sbjct: 1   MAALTLQGVKKTYDGKQFVLHGIDVDVADGEFVVMVGPSGCGKSTLLRMVAGLERISEGS 60

Query: 60  LLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAE 119
           + I  + VN L PKDR++ MVFQ+YALYPHM+VAENM + LK+A VD+ +I +RV+A A+
Sbjct: 61  ISIAGKVVNQLEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAKRVDAAAQ 120

Query: 120 ILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARL 179
           IL+L+ LL+RKP++LSGGQRQRVA+GR +VREP VFLFDEPLSNLDA LRVQMR+EI RL
Sbjct: 121 ILELEALLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQRL 180

Query: 180 HQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQM 239
           H R+ +T +YVTHDQ+EAMTLA +++V+N G   Q+G P  +Y  P   FVA F+GSP M
Sbjct: 181 HARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVASFIGSPGM 240

Query: 240 NFVEVRAISASPETVTIELPSGYPLTLPVD-----GSAVSPGDPLTLGIRPEHFVMPDEA 294
           N +E R    S +    E+    P  LP+      G  V+ G   TLGIRPEH + P +A
Sbjct: 241 NLLEGR---VSDDGAFFEVAGNGP-KLPLTDVASIGREVARGREWTLGIRPEH-MSPGQA 295

Query: 295 DFTFHGQITV--AERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHL 352
           D   H  +TV   E LG  NL +    +    +T+ +    R   GE     L A   H 
Sbjct: 296 DAP-HATLTVDSCELLGADNLAHGRWGKHD--VTVRLPHAHRPAAGEALQVALPARHLHF 352

Query: 353 F 353
           F
Sbjct: 353 F 353


Lambda     K      H
   0.322    0.139    0.405 

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: 391
Number of extensions: 16
Number of successful extensions: 3
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: 371
Length of database: 362
Length adjustment: 30
Effective length of query: 341
Effective length of database: 332
Effective search space:   113212
Effective search space used:   113212
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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