Alignments for a candidate for prpD in Halomonas xinjiangensis TRM 0175

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpD in Halomonas xinjiangensis TRM 0175

Align Citrate/2-methylcitrate dehydratase; EC 4.2.1.- (characterized)
to candidate WP_043530518.1 JH15_RS12230 2-methylcitrate dehydratase

Query= SwissProt::P45859
         (472 letters)



>NCBI__GCF_000759345.1:WP_043530518.1
          Length = 494

 Score =  618 bits (1593), Expect = 0.0
 Identities = 301/482 (62%), Positives = 379/482 (78%), Gaps = 13/482 (2%)

Query: 2   PKTDRVIEEITDYVLEKEITSAEAYTTAGHVLLDTLGCGILALRYPECTKLLGPIVPGTT 61
           P  D  +++I DYVLE  I S EA  TA + L+DTLGCG+LALR+PECTK LGP+V GT 
Sbjct: 11  PDYDSELQQIADYVLEYRIESPEALETARNCLIDTLGCGLLALRFPECTKHLGPLVEGTV 70

Query: 62  VPNGSKVPGTSYVLDPVRAAFNIGCMIRWLDYNDTWLAAEWGHPSDNLGGILAAADYVSR 121
           VPNGS+VPGTS+ LDPV+AA++IGC +RWLDYNDTWLAAEWGHPSDNLGGILA AD++S+
Sbjct: 71  VPNGSRVPGTSFRLDPVKAAWDIGCTVRWLDYNDTWLAAEWGHPSDNLGGILAVADHLSQ 130

Query: 122 VRLSEGKEPLTVRDVLEMMIKAHEIQGVLALENSLNRVGLDHVLFVKVATTAVAAKLLGG 181
            R+S+G+  L++RDVLE M+ AHEIQGVLALENS NRVGLDHV+ VKVA+TAVAAKL+G 
Sbjct: 131 KRISQGEAALSMRDVLEAMVMAHEIQGVLALENSFNRVGLDHVVLVKVASTAVAAKLMGA 190

Query: 182 GREEIKNALSNAWIDNAALRTYRHSPNTGSRKSWAAGDATSRGVHLALMSLKGEMGYPTA 241
            R++I +ALS+AW+D  +LRTYRH+PN GSRKSWAAGDATSRGV LA ++L+GEMG P+A
Sbjct: 191 NRDQILSALSHAWVDGQSLRTYRHAPNAGSRKSWAAGDATSRGVRLADIALRGEMGVPSA 250

Query: 242 LSAPGWGFQDVLFNK------------KEIKLARPLDAYVMENVLFKVSYPAEFHAQTAA 289
           L+A  WGF DVLF K            +   + +P   YVMENVLFK+++PAEFHAQTA 
Sbjct: 251 LTATQWGFYDVLFAKTNKDQQIKPEPQRRFSIPQPYGTYVMENVLFKIAFPAEFHAQTAC 310

Query: 290 ESAVILHPQVKNRIDEIDRVVIRTHESAIRIIDKKGPLHNPADRDHCLQYITAIGLLFGD 349
           E+AV LHP+VK+R+DEI+R+V+ THESAIRII K+G L NPADRDHCLQY+ A+ L+FGD
Sbjct: 311 EAAVRLHPEVKDRLDEIERIVVTTHESAIRIISKEGELANPADRDHCLQYMVAVPLMFGD 370

Query: 350 ITAQHYEAE-TANDPRIDKLRDKMEVTENKTYTEDYLKPDKRSISNAVQVHFKDGTSTEM 408
           +TA+HYE    A  PRID LR KMEVTE+  +T++YL+ DKRSI+NA+QV F+DG+ TE 
Sbjct: 371 LTAEHYEDRFHAEHPRIDTLRAKMEVTEDPRFTQEYLEADKRSIANAIQVFFQDGSKTEQ 430

Query: 409 VECEFPLGHRFRREEAVPKLLEKFSDNLKTHFPDKQHKHIYERCTSYETLQTMRVNEFVD 468
           V  E+PLGHR RR+E +P L+EKF  NL T FP ++   I   CT  + L+   V+ F+D
Sbjct: 431 VVVEYPLGHRRRRQEGIPLLVEKFKANLATRFPVQRCGEIVSLCTDKQALEATPVHRFMD 490

Query: 469 MF 470
           ++
Sbjct: 491 LW 492


Lambda     K      H
   0.319    0.135    0.402 

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: 688
Number of extensions: 22
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: 472
Length of database: 494
Length adjustment: 34
Effective length of query: 438
Effective length of database: 460
Effective search space:   201480
Effective search space used:   201480
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: 52 (24.6 bits)

Align candidate WP_043530518.1 JH15_RS12230 (2-methylcitrate dehydratase)
to HMM TIGR02330 (prpD: 2-methylcitrate dehydratase (EC 4.2.1.79))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02330.hmm
# target sequence database:        /tmp/gapView.766400.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02330  [M=468]
Accession:   TIGR02330
Description: prpD: 2-methylcitrate dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-270  883.8   0.0   1.5e-270  883.6   0.0    1.0  1  NCBI__GCF_000759345.1:WP_043530518.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000759345.1:WP_043530518.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  883.6   0.0  1.5e-270  1.5e-270       1     468 []      14     494 .]      14     494 .] 0.99

  Alignments for each domain:
  == domain 1  score: 883.6 bits;  conditional E-value: 1.5e-270
                             TIGR02330   1 davlediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsyqldp 73 
                                           d++l++iadyvley+i+s+ea++tar++l+dtlgcgllal++pectk+lgp+vegt+vpng+rvpgts++ldp
  NCBI__GCF_000759345.1:WP_043530518.1  14 DSELQQIADYVLEYRIESPEALETARNCLIDTLGCGLLALRFPECTKHLGPLVEGTVVPNGSRVPGTSFRLDP 86 
                                           7899********************************************************************* PP

                             TIGR02330  74 vkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevleamikaheiqgvl 146
                                           vkaa++ig+ vrwldyndtwlaaewghpsdnlggilavad+ls+kri++g++ l++++vleam++aheiqgvl
  NCBI__GCF_000759345.1:WP_043530518.1  87 VKAAWDIGCTVRWLDYNDTWLAAEWGHPSDNLGGILAVADHLSQKRISQGEAALSMRDVLEAMVMAHEIQGVL 159
                                           ************************************************************************* PP

                             TIGR02330 147 alensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrhapntgsrkswaagdatsr 219
                                           alensfnrvgldhv+lvkvastav+akl+ga+r++il+alsha+vdgq+lrtyrhapn+gsrkswaagdatsr
  NCBI__GCF_000759345.1:WP_043530518.1 160 ALENSFNRVGLDHVVLVKVASTAVAAKLMGANRDQILSALSHAWVDGQSLRTYRHAPNAGSRKSWAAGDATSR 232
                                           ************************************************************************* PP

                             TIGR02330 220 gvrlalialkgemgypsalsapvwgfedvlfkke............klklareygsyvmenvlfkisfpaefh 280
                                           gvrla+ial+gemg+psal+a++wgf+dvlf k+            +++++++yg+yvmenvlfki+fpaefh
  NCBI__GCF_000759345.1:WP_043530518.1 233 GVRLADIALRGEMGVPSALTATQWGFYDVLFAKTnkdqqikpepqrRFSIPQPYGTYVMENVLFKIAFPAEFH 305
                                           *******************************99999************************************* PP

                             TIGR02330 281 aqtaveaavklheevkerldeierivitthesairiidkkgplanpadrdhclqylvavpllfgdlvaedyed 353
                                           aqta+eaav+lh+evk+rldeieriv+tthesairii+k+g lanpadrdhclqy+vavpl+fgdl+ae+yed
  NCBI__GCF_000759345.1:WP_043530518.1 306 AQTACEAAVRLHPEVKDRLDEIERIVVTTHESAIRIISKEGELANPADRDHCLQYMVAVPLMFGDLTAEHYED 378
                                           ************************************************************************* PP

                             TIGR02330 354 a.vaadpridelreklevvedkrysreyleadkrsianavevffkdgskteeveveyplghrrrrdegipklv 425
                                             +a++prid+lr k+ev+ed+r+++eyleadkrsiana++vff+dgskte+v+veyplghrrrr+egip+lv
  NCBI__GCF_000759345.1:WP_043530518.1 379 RfHAEHPRIDTLRAKMEVTEDPRFTQEYLEADKRSIANAIQVFFQDGSKTEQVVVEYPLGHRRRRQEGIPLLV 451
                                           999********************************************************************** PP

                             TIGR02330 426 dkfkanlatkfsskkqerilelcldqakleatpvnefldlfvi 468
                                           +kfkanlat+f+ +++ +i  lc+d++ leatpv +f+dl+ i
  NCBI__GCF_000759345.1:WP_043530518.1 452 EKFKANLATRFPVQRCGEIVSLCTDKQALEATPVHRFMDLWTI 494
                                           ****************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (494 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 29.73
//
[ok]

This GapMind analysis is from Sep 24 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 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