GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PRO3 in Amantichitinum ursilacus IGB-41

Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate WP_053936293.1 WG78_RS02925 pyrroline-5-carboxylate reductase

Query= BRENDA::O87725
         (266 letters)



>NCBI__GCF_001294205.1:WP_053936293.1
          Length = 263

 Score =  210 bits (535), Expect = 2e-59
 Identities = 117/262 (44%), Positives = 162/262 (61%), Gaps = 2/262 (0%)

Query: 5   IGFIGCGNMAQAMISALVKSKLIESNQIIVSNRSKNILEKMNKEYGITIAANNIEVAEKC 64
           IGFIG GNMA AMI+ L  S      QI   NRS   L  +   YG+ IA +  ++A + 
Sbjct: 3   IGFIGTGNMASAMIAGLHSSH--PDWQIHGFNRSMGKLTDLQTRYGLQIAQSLEDLAARA 60

Query: 65  DIVFLAVKQNLYEMVMKEIKDSVTKDKIFVSIAPGKTMEFLEAHLGAYAKILRTMPNTPS 124
           D++ LAVK   Y+ ++  +   +      V++A G T+  +++H+G    I+R+MPNTP+
Sbjct: 61  DVLVLAVKPQGYDAMLATLAPPLQARHTLVTVAVGYTIARVQSHIGTQTHIVRSMPNTPA 120

Query: 125 MVSEGMTAICPNSNIASEELELLVKLIESFGAVEIIEEKLFDAVVAVSGSSPAYVFMFIE 184
            V  GM+A+C ++ +       +  + ESFG    I E  FD   A++GSSPA+V+M IE
Sbjct: 121 SVGAGMSALCGSAGLPEARRSDVTAVFESFGRAVWIAEGQFDVFSAIAGSSPAWVYMMIE 180

Query: 185 AMADAAVIQGMPRAQAYRFAAQAVLGSAKMVLESKSHPGELKDMVCSPGGTTIEAVAVLE 244
           AMADAAV  GMPRAQAY   +QAVLGSA++V +S  HPG LKD VCSPGGTTI  VA LE
Sbjct: 181 AMADAAVQNGMPRAQAYAVISQAVLGSAQLVRDSGQHPGVLKDQVCSPGGTTIAGVAALE 240

Query: 245 ERGMRSAVIEAMRKCAQKSKEM 266
           + GMR+A  EA+     ++K +
Sbjct: 241 KAGMRNAWFEAVNATLARTKAL 262


Lambda     K      H
   0.317    0.130    0.349 

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: 161
Number of extensions: 5
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: 266
Length of database: 263
Length adjustment: 25
Effective length of query: 241
Effective length of database: 238
Effective search space:    57358
Effective search space used:    57358
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: 47 (22.7 bits)

Align candidate WP_053936293.1 WG78_RS02925 (pyrroline-5-carboxylate reductase)
to HMM TIGR00112 (proC: pyrroline-5-carboxylate reductase (EC 1.5.1.2))

# 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/TIGR00112.hmm
# target sequence database:        /tmp/gapView.1811756.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00112  [M=263]
Accession:   TIGR00112
Description: proC: pyrroline-5-carboxylate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    8.6e-83  264.0   1.8    9.6e-83  263.8   1.8    1.0  1  NCBI__GCF_001294205.1:WP_053936293.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001294205.1:WP_053936293.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.8   1.8   9.6e-83   9.6e-83       1     263 []       3     262 ..       3     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: 263.8 bits;  conditional E-value: 9.6e-83
                             TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdle 73 
                                           i++iG Gnm++a+++gl+++    + +i+  +rs  kl++l +++g + +++ e +++ adv++lavKPq  +
  NCBI__GCF_001294205.1:WP_053936293.1   3 IGFIGTGNMASAMIAGLHSS--HPDWQIHGFNRSMGKLTDLQTRYGLQIAQSLEDLAARADVLVLAVKPQGYD 73 
                                           89**************9998..4479*********************************************** PP

                             TIGR00112  74 evlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelvee 146
                                           ++la+l+    ++ ++l++++ G ti+++++++++++++vR mPNt+a+vgag++a++ s+   e++++ v++
  NCBI__GCF_001294205.1:WP_053936293.1  74 AMLATLAP-PLQARHTLVTVAVGYTIARVQSHIGTQTHIVRSMPNTPASVGAGMSALCGSAGLPEARRSDVTA 145
                                           *******9.4457899***********************************************999******* PP

                             TIGR00112 147 llkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehp 219
                                           +++++G +v+++e ++d + a++GS+PA+v+++iea+ada+v++G+pr++a+++++q++ G+a+l+  sg+hp
  NCBI__GCF_001294205.1:WP_053936293.1 146 VFESFGRAVWIAEGQFDVFSAIAGSSPAWVYMMIEAMADAAVQNGMPRAQAYAVISQAVLGSAQLVRDSGQHP 218
                                           ************************************************************************* PP

                             TIGR00112 220 alLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263
                                            +Lkd+V+sPgGtTiag+a+Le++g+r+a  eav+a+ +r++ L
  NCBI__GCF_001294205.1:WP_053936293.1 219 GVLKDQVCSPGGTTIAGVAALEKAGMRNAWFEAVNATLARTKAL 262
                                           ****************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (263 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 9.97
//
[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