Alignments for a candidate for hutU in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutU in Flavobacterium beibuense F44-8

Align Urocanate hydratase (EC 4.2.1.49) (characterized)
to candidate WP_035135947.1 Q763_RS15515 urocanate hydratase

Query= reanno::SB2B:6937476
         (670 letters)



>NCBI__GCF_000769915.1:WP_035135947.1
          Length = 662

 Score = 1059 bits (2739), Expect = 0.0
 Identities = 510/661 (77%), Positives = 574/661 (86%)

Query: 5   MTFAEQIKQGIPAELPSPKPYPADANRAPKRKDILTAAEKQLAVRNALRYFPAEWHQELA 64
           MTF EQI++GIP+ LP PKPY    N APKRK+IL+A EK+LA+RNALRYF  + H ELA
Sbjct: 1   MTFKEQIQEGIPSVLPQPKPYDPTINHAPKRKEILSAEEKKLALRNALRYFEPQHHAELA 60

Query: 65  AEFAKELNDFGRIYMYRFKPEYAMKARAISEYPAKCEQAAAIMLMVDNNLDPAVAQHPEE 124
            EFA EL  +GRIYMYRF+P+Y M AR ISEYP K EQA AIMLM+ NNLD AVAQHP E
Sbjct: 61  KEFADELEKYGRIYMYRFRPDYEMYARPISEYPGKSEQAKAIMLMIQNNLDYAVAQHPHE 120

Query: 125 LITYGGNGAVFQNWAQYRLTMKYLSEMEADQTLHLYSGHPMGLFPSSVDAPRVVVTNGMM 184
           LITYGGNGAVFQNWAQYRL MKYLSEM  +QTL +YSGHPMGLFPS  DAPRVVVTNGMM
Sbjct: 121 LITYGGNGAVFQNWAQYRLVMKYLSEMTEEQTLVMYSGHPMGLFPSHKDAPRVVVTNGMM 180

Query: 185 IPNYSKPDDWERFNALGVTQYGQMTAGSFMYIGPQGIVHGTTITVMNGFRKVLEKGDSPK 244
           IPNYSKPDDWE+FNALGVTQYGQMTAGS+MYIGPQGIVHGTTITVMNG RK+ + G+  +
Sbjct: 181 IPNYSKPDDWEKFNALGVTQYGQMTAGSYMYIGPQGIVHGTTITVMNGGRKISKNGEGLE 240

Query: 245 GKIFLTAGLGGMSGAQPKAGNIAGCITVCAEVNPKAATKRHAQGWVDELIDNMDALVARV 304
           GK+F+T+GLGGMSGAQPKAGNIAGCITVCAEVNPKA   RH+QGWVDE++ + DALV RV
Sbjct: 241 GKVFVTSGLGGMSGAQPKAGNIAGCITVCAEVNPKAVHTRHSQGWVDEVVTDTDALVKRV 300

Query: 305 KQAQANEEVVSIAFIGNVVNVWEAFDEHDIFVHLGSDQTSLHNPWSGGYYPVDISYDESN 364
            +A+AN+EVVSIA+ GN+V+VWE FDE +I++ LGSDQTSLHNPW+GGYYP  IS++ESN
Sbjct: 301 LEAKANKEVVSIAYQGNIVDVWEKFDEENIYIDLGSDQTSLHNPWAGGYYPAGISFEESN 360

Query: 365 RLIREEPELFKTKVQATLKRHADAINRHTAKGTYFFDYGNAFLLEASRAGGDVMAENGID 424
           RL+ EEPE F+ KVQ TL+RHA AIN+HTAKGTYFFDYGNAFLLEASRAG D+MAENGID
Sbjct: 361 RLMAEEPETFREKVQETLRRHAAAINKHTAKGTYFFDYGNAFLLEASRAGADIMAENGID 420

Query: 425 FKYPSYVQDILGPMCFDYGFGPFRWVCTSGNSADLDRTDAIAAEVLARIMAEAPAEIQQQ 484
           FKYPSYVQDI+GPMCFDYGFGPFRWVC SG   DL +TDAIA  +L  +   APAEI+QQ
Sbjct: 421 FKYPSYVQDIMGPMCFDYGFGPFRWVCASGKPEDLAKTDAIALNILEEMSTTAPAEIKQQ 480

Query: 485 MQDNITWIKDAKQNKLVVGSQARILYADAEGRMEIAKAFNDAISRGEIGPVVLGRDHHDV 544
           MQDNI WIK A++NKLVVGSQARILYADAEGR++IA+AFN AI++GEIG VVLGRDHHDV
Sbjct: 481 MQDNIKWIKGAQENKLVVGSQARILYADAEGRIKIAEAFNQAIAKGEIGYVVLGRDHHDV 540

Query: 545 SGTDSPFRETSNIYDGSRFTADMAIHNVIGDSFRGATWVSIHNGGGVGWGEVINGGFGML 604
           SGTDSP+RETSNIYDGSRFTADMAIHNVIGDSFRGATWVSIHNGGGVGWGEVINGGFGM+
Sbjct: 541 SGTDSPYRETSNIYDGSRFTADMAIHNVIGDSFRGATWVSIHNGGGVGWGEVINGGFGMV 600

Query: 605 LDGTEAAERRLKSMLLFDVNNGIARRSWARNEEANFAIKREMARTPKLKVTLANSVDDDI 664
           LDG+  A RRL+SML +DVNNGIARR WARNE A FAIKR M   P LKVT+ N VDD +
Sbjct: 601 LDGSSDASRRLESMLFWDVNNGIARRGWARNEGAVFAIKRAMEVQPLLKVTIPNMVDDAL 660

Query: 665 I 665
           +
Sbjct: 661 L 661


Lambda     K      H
   0.318    0.134    0.404 

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: 1359
Number of extensions: 45
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: 670
Length of database: 662
Length adjustment: 38
Effective length of query: 632
Effective length of database: 624
Effective search space:   394368
Effective search space used:   394368
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 (21.7 bits)
S2: 54 (25.4 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