Alignments for a candidate for glpV in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpV in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for Glycerol, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_03729 H281DRAFT_03729 carbohydrate ABC transporter substrate-binding protein, CUT1 family

Query= reanno::acidovorax_3H11:Ac3H11_796
         (577 letters)



>FitnessBrowser__Burk376:H281DRAFT_03729
          Length = 579

 Score =  928 bits (2398), Expect = 0.0
 Identities = 440/580 (75%), Positives = 495/580 (85%), Gaps = 4/580 (0%)

Query: 1   MKMQFKAIAFAAAAL---AMGQAAWAGEAEAKKWIDSEFQPSTLNKDQQMAEMKWFIDAA 57
           M+ + + +A A A +   A+   A AG  EA+KW+DSEFQPSTL+K QQM EMKWF+D +
Sbjct: 1   MQQRRRIVALAVAGIVSGALANQAQAGMPEAQKWVDSEFQPSTLSKQQQMDEMKWFVDTS 60

Query: 58  KKLQAKGVKEISVVSETITTHEYESKTLAKAFEEITGIKVKHDLIQEGDVVEKLQTSMQS 117
            KL+++GVKEI VVSETI TH YESKTLAKAF EITGI+VKHD+IQEGDVVEKLQTSMQS
Sbjct: 61  AKLKSQGVKEIHVVSETIDTHIYESKTLAKAFTEITGIQVKHDIIQEGDVVEKLQTSMQS 120

Query: 118 GKSIYDGWISDSDLIGTHYRYGKIMNLTDYMGGAGKEWTNPGIDLKDYIGTKFTTGPDGK 177
           G+SIYDGWISDSDLIGTHYRYG I+ L+DYM G GK++TNPG+D+KD+IGT FTT PD K
Sbjct: 121 GQSIYDGWISDSDLIGTHYRYGVIVPLSDYMTGEGKDYTNPGLDIKDFIGTSFTTAPDKK 180

Query: 178 LYQLPDQQFANLYWFRADLFDRKDIKDKFKAKYGYDLGVPLNWSAYEDIAEFFTNDVKNI 237
           LYQLPDQQFANLYWFRAD F RKD++DKFKAKYGY+LGVP+NWSAYEDIAEFFTNDVKNI
Sbjct: 181 LYQLPDQQFANLYWFRADWFARKDLQDKFKAKYGYELGVPVNWSAYEDIAEFFTNDVKNI 240

Query: 238 DGKPIYGHMDYGKKDPSLGWRFTDAWLSMAGTADIGAPNGLPIDEWGIRVADDKCTPVGA 297
           DG  +YGHMDYGKKDPSLGWRFTDAWLSMAG AD G PNG+P+DEWGIRV  D C PVGA
Sbjct: 241 DGDKVYGHMDYGKKDPSLGWRFTDAWLSMAGEADKGIPNGMPVDEWGIRVTPDGCHPVGA 300

Query: 298 SVARGGATNSPAAVYALTKYVDWMKKYAPKEATGMTFGEAGPVPAQGQIAQQIFWYTAFT 357
           SV+RGG TNSPAAVYA TKY+DW+KKYAP EA+GMTF EAGPVPAQG+IAQQ+FWYTAFT
Sbjct: 301 SVSRGGGTNSPAAVYATTKYIDWLKKYAPPEASGMTFSEAGPVPAQGKIAQQVFWYTAFT 360

Query: 358 ADMTKPGLPVVNADGTPKWRMAPGPNGPYWKQGMQNGYQDVGSWTFFKDHDANKTAAAWL 417
           A M KPG  V N DGTPKWRMAP P+G YWK GMQNGYQDVGSWTFFK    N+ AAAWL
Sbjct: 361 ASMLKPG-NVTNPDGTPKWRMAPSPHGAYWKDGMQNGYQDVGSWTFFKSTPPNQRAAAWL 419

Query: 418 YAQFVTAKTTSLKKTMVGLTPIRESDIQSKAMTDMAPKLGGLVEFYRSPARVAWSPTGTN 477
           YAQFVTAK+ SLKK++VGLT IR+SDI S   T  A K GGL+EFYRSPARVAW+PTG N
Sbjct: 420 YAQFVTAKSVSLKKSIVGLTFIRDSDIHSDYFTKNADKYGGLIEFYRSPARVAWTPTGNN 479

Query: 478 VPDYPKLAQLWWKNVAQAVTGEKTPQGAMDTLADEMDQVMARLERAGMAHCAPKLNAKSD 537
           VPDYPK+AQLWWKNV  AV GEK+PQ AMD LA EMDQV++RL+RAGM  CAP+LNA+SD
Sbjct: 480 VPDYPKMAQLWWKNVGTAVAGEKSPQAAMDNLAKEMDQVLSRLQRAGMKVCAPELNAQSD 539

Query: 538 PNKWLSDKQAPWKKLANEKPKGETIAYGTLLQAWKDGKTR 577
           P+KWLSD+ APWKKLANEKPKGET+ Y  LL AWK GK R
Sbjct: 540 PSKWLSDQHAPWKKLANEKPKGETVKYEQLLSAWKAGKVR 579


Lambda     K      H
   0.315    0.132    0.412 

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: 1392
Number of extensions: 66
Number of successful extensions: 2
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: 577
Length of database: 579
Length adjustment: 36
Effective length of query: 541
Effective length of database: 543
Effective search space:   293763
Effective search space used:   293763
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. 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 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