Alignments for a candidate for xad in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for xad in Pseudomonas fluorescens GW456-L13

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate PfGW456L13_3320 L-arabonate dehydratase (EC 4.2.1.25)

Query= reanno::pseudo6_N2E2:Pf6N2E2_1668
         (594 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3320
          Length = 578

 Score =  436 bits (1122), Expect = e-126
 Identities = 258/599 (43%), Positives = 356/599 (59%), Gaps = 26/599 (4%)

Query: 1   MSDTPKHRLRSEQWFNDPAHADMTALYVERYM-NYGMTREELQSGRPIIGIAQTGSDLTP 59
           MSD  K  LRS QWF     AD        +M N G+   +   G+PIIGI  T S+LTP
Sbjct: 1   MSDK-KPTLRSAQWFGT---ADKNGFMYRSWMKNQGIADHQFH-GKPIIGICNTWSELTP 55

Query: 60  CNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPL 119
           CN H  ++A+ VK G+ +AGG P+EFPV    E + RPTA L RNLA + + E + G P+
Sbjct: 56  CNAHFRQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPI 115

Query: 120 DGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAA 179
           DGVVL TGCDKTTPA LM AA+ D+PAIV++GGPML+G HKG+ IGSGTV+W     + A
Sbjct: 116 DGVVLLTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGKDIGSGTVVWQLSEQVKA 175

Query: 180 GEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAY 239
           G I  + F+      S S G CNTMGTA +M  +AEALG SLP  A+IPA    R  +A+
Sbjct: 176 GTISIDDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAH 235

Query: 240 ATGKRICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLED 299
            +G R  ++VR+D++ S+I+T++AFENAI V +A+G S+N   HL AIA  +GVEL L+D
Sbjct: 236 MSGMRAVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDD 295

Query: 300 WQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRL-HEDCATVSGKTIGEI 358
           W RIG  +P +V+  P+G++L E F+ AGG+P+V+  L +A  + + +  TV+GK+IGE 
Sbjct: 296 WTRIGRGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKSIGEN 355

Query: 359 VSNS-LTSNTDVIHPFDTPLKHRAGFIVLSGNFFD-SAIMKMSVVGEAFRKTYLSEPGAE 416
             ++ +    +VI   D P++   G  VL GN     A++K S       +         
Sbjct: 356 TRDAPIYGEDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAATPELMQ--------- 406

Query: 417 NSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIK 476
                RA+VFE  + Y ARI+DP LD+D   ILV++  G  GYPG AEV NM  PA L+ 
Sbjct: 407 --HRGRAVVFENFDMYKARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLA 464

Query: 477 QGIDSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDD 536
           QG+  +  + D R SGT+    +L+++PEAA GG LA +K  D +++D  +  ++L I D
Sbjct: 465 QGVTDMVRISDARMSGTAYGTVVLHVAPEAAAGGPLAAVKEGDWIELDCASGRLHLDIAD 524

Query: 537 AEMAQRRREWIPNIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGE-PRHSH 594
            E+A R  +  P        +++LY   V Q   G           V  R  E PRHSH
Sbjct: 525 TELAARMADLQPPQNLIVGGYRQLYIDHVLQADQG-----CDFDFLVGCRGAEVPRHSH 578


Lambda     K      H
   0.319    0.135    0.407 

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: 966
Number of extensions: 62
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: 594
Length of database: 578
Length adjustment: 37
Effective length of query: 557
Effective length of database: 541
Effective search space:   301337
Effective search space used:   301337
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 (21.7 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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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