GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Brevibacterium jeotgali SJ5-8

Align Probable 2-methylisocitrate lyase 2; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate WP_101586816.1 BJEO58_RS00620 methylisocitrate lyase

Query= SwissProt::Q8NSL2
         (307 letters)



>NCBI__GCF_900169175.1:WP_101586816.1
          Length = 301

 Score =  333 bits (855), Expect = 2e-96
 Identities = 172/304 (56%), Positives = 211/304 (69%), Gaps = 3/304 (0%)

Query: 1   MAGLFSSAVAPTERRKALRAALAAPEIARMPGAFSPLAARAIQEAGFEGVYVSGAVVAAD 60
           M G   +A A   RR   RA L + E+ + PGA +PL A  I++ GFEGVY+SG   +A 
Sbjct: 1   MLGATKTAAA---RRADFRALLDSGEVVQFPGAINPLNAMLIEQTGFEGVYISGGAFSAA 57

Query: 61  LALPDIGLTTLTEVAHRSRQIARVTDLPVLVDADTGFGEPMSAARTVSELEDAGVAGCHL 120
             LPDIGLTTLTEV    R IARVT+LP  +DADTG+GE M+ ARTV E EDAG++G HL
Sbjct: 58  QGLPDIGLTTLTEVVDHGRSIARVTNLPTFIDADTGWGEAMNVARTVQEFEDAGLSGIHL 117

Query: 121 EDQVNPKRCGHLDGKEVVGTDIMVRRIAAAVNERRDEQFVICARTDAAGVEGIDSAIERA 180
           EDQVNPKRCGHLDGKEVV T  MV+RI+AA   RRDE F++CARTD+   EG+D+AI+RA
Sbjct: 118 EDQVNPKRCGHLDGKEVVTTAEMVKRISAAAKGRRDENFILCARTDSRAGEGLDAAIDRA 177

Query: 181 KAYADAGADMIFTEALYSPADFEKFRAAVDIPLLANMTEFGKTELLPAQLLEDIGYNAVI 240
           +AY  AGADMIF EA+    +FE F  AVD P+LANMTEFGK+EL   + L D G   VI
Sbjct: 178 RAYVAAGADMIFPEAMRDLGEFETFANAVDAPILANMTEFGKSELFTTKQLADAGVRVVI 237

Query: 241 YPVTLLRIAMGQVEQALGDIANTGIQTDWVDRMQHRSRLYELLRYNEYNAFDQQVFTYSA 300
           YPVT LR+AMG +   L  I + G Q   VDRMQ R+ LYE + Y  YN+FD  VF +S 
Sbjct: 238 YPVTTLRLAMGAITDGLQAIRSEGTQASVVDRMQTRADLYETVDYEAYNSFDSAVFNFSQ 297

Query: 301 DSYK 304
           + ++
Sbjct: 298 EGHQ 301


Lambda     K      H
   0.320    0.134    0.382 

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: 296
Number of extensions: 11
Number of successful extensions: 1
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: 307
Length of database: 301
Length adjustment: 27
Effective length of query: 280
Effective length of database: 274
Effective search space:    76720
Effective search space used:    76720
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_101586816.1 BJEO58_RS00620 (methylisocitrate lyase)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

# 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/TIGR02317.hmm
# target sequence database:        /tmp/gapView.2739434.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02317  [M=285]
Accession:   TIGR02317
Description: prpB: methylisocitrate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.6e-129  415.9   0.5   4.2e-129  415.7   0.5    1.0  1  NCBI__GCF_900169175.1:WP_101586816.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900169175.1:WP_101586816.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.7   0.5  4.2e-129  4.2e-129       2     284 ..      12     294 ..      11     295 .. 0.99

  Alignments for each domain:
  == domain 1  score: 415.7 bits;  conditional E-value: 4.2e-129
                             TIGR02317   2 gkalrellkkedilqipGainalvallaekaGfeavYlsGaalaaslglPDlglttleevaeearritrvtkl 74 
                                           ++ +r+ll++++++q pGain+l a+l+e++Gfe+vY+sG+a++a  glPD+glttl+ev+ + r+i+rvt+l
  NCBI__GCF_900169175.1:WP_101586816.1  12 RADFRALLDSGEVVQFPGAINPLNAMLIEQTGFEGVYISGGAFSAAQGLPDIGLTTLTEVVDHGRSIARVTNL 84 
                                           678********************************************************************** PP

                             TIGR02317  75 pllvDaDtGfGealnvartvkeleeagvaavhieDqvapkkCGhldgkelvskeemvkkikaavkakkdedfv 147
                                           p+++DaDtG+Gea+nvartv+e+e+ag++++h+eDqv+pk+CGhldgke+v++ emvk+i aa+k+++de+f+
  NCBI__GCF_900169175.1:WP_101586816.1  85 PTFIDADTGWGEAMNVARTVQEFEDAGLSGIHLEDQVNPKRCGHLDGKEVVTTAEMVKRISAAAKGRRDENFI 157
                                           ************************************************************************* PP

                             TIGR02317 148 liaRtDaraveGldaaieRakaYveaGadaiftealeseeefrefakavkvpllanmtefGktplltadelee 220
                                           l+aRtD+ra eGldaai+Ra+aYv aGad+if+ea++++ ef++fa+av++p+lanmtefGk+ l+t+++l++
  NCBI__GCF_900169175.1:WP_101586816.1 158 LCARTDSRAGEGLDAAIDRARAYVAAGADMIFPEAMRDLGEFETFANAVDAPILANMTEFGKSELFTTKQLAD 230
                                           ************************************************************************* PP

                             TIGR02317 221 lgykiviyPvtalRaalkaaekvyeelkkkGtqkelldklqtRkelYellgyedyekkdkelfk 284
                                           +g+++viyPvt+lR+a++a+++ ++ ++ +Gtq +++d++qtR++lYe+++ye+y+++d+ +f+
  NCBI__GCF_900169175.1:WP_101586816.1 231 AGVRVVIYPVTTLRLAMGAITDGLQAIRSEGTQASVVDRMQTRADLYETVDYEAYNSFDSAVFN 294
                                           ************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (301 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: 15.58
//
[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:

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:

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:

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:

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