Alignments for a candidate for uxaA in Leeuwenhoekiella blandensis MED217

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxaA in Leeuwenhoekiella blandensis MED217

Align Altronate dehydratase (EC 4.2.1.7) (characterized)
to candidate WP_009779318.1 MED217_RS04610 altronate dehydratase

Query= reanno::Pedo557:CA265_RS19875
         (548 letters)



>NCBI__GCF_000152985.1:WP_009779318.1
          Length = 538

 Score =  606 bits (1562), Expect = e-178
 Identities = 295/548 (53%), Positives = 394/548 (71%), Gaps = 10/548 (1%)

Query: 1   MVTRILKIHPNDNVLVALQNLAKGETVIYDGHEYILQDDIQAKHKFFMQDMNAGDHIIMY 60
           M ++++K+HP+DNV VAL +L  G+ V ++G    +  D +AKHK  + ++ A D I MY
Sbjct: 1   MKSKLIKVHPDDNVAVALVDLFAGDVVEFEGQSLKILTDSKAKHKIALVNLKADDPIFMY 60

Query: 61  GVLVGKAQHFILKGGLMDTENTKHASDPYEFRPYHYEWHAPDVSKFEGRTFNGYIRSDGR 120
           GVLVGKA   I  GGL+ TEN KH ++    +     W APD+SK++ RTF GY R DG+
Sbjct: 61  GVLVGKALSAIDVGGLLTTENVKHEANSVSQKTETTSWTAPDISKWKDRTFMGYHREDGQ 120

Query: 121 VGTANYWLFIPTVFCENRNLDVIREALHNELGYAVTDKYKSYAHQLVEAYKNGEILAEAD 180
           VGT N WLF P VFCENRN++++++    EL +    K +     L+        +AE +
Sbjct: 121 VGTQNVWLFFPLVFCENRNIELLKDVFEKELSFHKASKQRQLLRNLINGAPEDTAVAEIE 180

Query: 181 PSSIGLANPSANRVFKNVDGIKFLNHQGGCGGTRQDAAVLSKLLAAYADHPNVAGVTVLS 240
                        +F N++ +KF+ HQGGCGG RQD+  LSKLLA Y ++PNVAG TVLS
Sbjct: 181 EEQA---------IFDNIE-VKFITHQGGCGGIRQDSVSLSKLLAGYVNNPNVAGATVLS 230

Query: 241 LGCQNLQVKDFMDDLKHRSPNFDKPLFVFEQQQSQSEEQLVKEAIRKTFIGLTEINKIER 300
           LGCQNLQ+  F + L  +S    KP+ ++EQQQ  + ++++ + I+ +F G+ + N+I+R
Sbjct: 231 LGCQNLQIDIFKNALAEKSAAIKKPVLIYEQQQEGTVDEMLAKIIKDSFEGIKKANQIKR 290

Query: 301 QPAPLSKLVLGVKCGGSDGFSGISANPAVGYTSDLLVALGGTVLLAEFPELCGAEQQLID 360
           QPAP+SKL +G++CGGSDGFSGISANPA+GY SD+L A+GG+ +L+EFPELCG EQ+L++
Sbjct: 291 QPAPISKLKMGLECGGSDGFSGISANPALGYASDILAAVGGSPILSEFPELCGVEQELVN 350

Query: 361 RTKDETAARKFIQLMTAYNQSAENVGSGFFMNPSPGNIKDGLITDAIKSTGAAKKGGTSP 420
           R   +  A +F+ LM AY +SA + GSGF MNPSPGNIKDGLITDA+KS GAAKKGGTSP
Sbjct: 351 RCVSDEDAERFMHLMKAYEKSAVDAGSGFDMNPSPGNIKDGLITDAMKSAGAAKKGGTSP 410

Query: 421 VEDVLDYTEPATKPGLNLVCTPGNDVEATTGKAASGATLILFTTGLGTPTGNPVCPTIKV 480
           ++ +LDY E  TKPGLNL+CTPGNDVE+TT    SGA++++FTTGLGTPTGNP+ P +KV
Sbjct: 411 IQAILDYGEYVTKPGLNLLCTPGNDVESTTAMVGSGASVVVFTTGLGTPTGNPIAPVLKV 470

Query: 481 STNNALTKRMGDIIDINCGPVIEGEKTIEQMGEDILEYCIKAASGEVIPKAVLLNQDDFI 540
           ++N+ L +RM DIIDI+ G VI GEKTIE+MGE+ILE+ I+ ASGEV  KA  L QDDFI
Sbjct: 471 ASNSTLARRMPDIIDIDSGAVIRGEKTIEEMGEEILEHVIQVASGEVQSKADALGQDDFI 530

Query: 541 PWKRGVSL 548
           PWKRGVSL
Sbjct: 531 PWKRGVSL 538


Lambda     K      H
   0.317    0.136    0.400 

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: 806
Number of extensions: 28
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: 548
Length of database: 538
Length adjustment: 35
Effective length of query: 513
Effective length of database: 503
Effective search space:   258039
Effective search space used:   258039
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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