GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proC in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_018232723.1 THITHI_RS0108825 pyrroline-5-carboxylate reductase

Query= SwissProt::P22008
         (273 letters)



>NCBI__GCF_000378965.1:WP_018232723.1
          Length = 275

 Score =  263 bits (671), Expect = 4e-75
 Identities = 150/270 (55%), Positives = 189/270 (70%), Gaps = 2/270 (0%)

Query: 6   IAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAE-AVADA 64
           IAFIGAGNMA SLIGGL   G P   + A DP A QR  ++  +    V ++A+ AVA A
Sbjct: 5   IAFIGAGNMARSLIGGLIQDGWPEDALWAVDPDAAQREGVSRRWPRVHVHADADQAVAHA 64

Query: 65  DVVVLSVKPQAMKAVCQALAPALKPE-QLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTP 123
           DV+VL+VKPQ +  V + LA A++    L+VSIAAG+    +E WLG   PVVRCMPNTP
Sbjct: 65  DVLVLAVKPQVLGGVARGLAGAVQARGPLVVSIAAGVRGEDIERWLGGDLPVVRCMPNTP 124

Query: 124 ALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLL 183
           AL+  GA+ L ANA+VS+ Q   A  +L AVG+ +WLDDEA +DAVTA+SGSGPAY FL+
Sbjct: 125 ALVGSGATALVANARVSSDQKAVAESILRAVGLTVWLDDEAALDAVTALSGSGPAYCFLV 184

Query: 184 MQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKS 243
           M+AM DAG +LGL RETA  L LQTA GAA++AL SE + A LR RVTS  GTTE A++ 
Sbjct: 185 MEAMEDAGVQLGLPRETARLLALQTAFGAAKLALESEEDAATLRARVTSRGGTTEQALQV 244

Query: 244 FQANGFEALVEQALNAASQRSAELAEQLGQ 273
            ++ G   L+ +AL AA  RS ELA+QLG+
Sbjct: 245 LESGGLRELLARALTAARDRSRELADQLGR 274


Lambda     K      H
   0.315    0.127    0.348 

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: 195
Number of extensions: 4
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: 273
Length of database: 275
Length adjustment: 25
Effective length of query: 248
Effective length of database: 250
Effective search space:    62000
Effective search space used:    62000
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: 47 (22.7 bits)

Align candidate WP_018232723.1 THITHI_RS0108825 (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.aa/TIGR00112.hmm
# target sequence database:        /tmp/gapView.2114067.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.1e-84  268.7   0.1    3.5e-84  268.5   0.1    1.0  1  NCBI__GCF_000378965.1:WP_018232723.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000378965.1:WP_018232723.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.5   0.1   3.5e-84   3.5e-84       1     263 []       5     268 ..       5     268 .. 0.96

  Alignments for each domain:
  == domain 1  score: 268.5 bits;  conditional E-value: 3.5e-84
                             TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelg.vevtsdaeeavkeadvvllavKPqdl 72 
                                           ia+iGaGnm+++l+ gl++ g + ++ ++ +++ +++++    +   v+v++da++av++adv++lavKPq+l
  NCBI__GCF_000378965.1:WP_018232723.1   5 IAFIGAGNMARSLIGGLIQDGWP-EDALWAVDPDAAQREGVSRRWPrVHVHADADQAVAHADVLVLAVKPQVL 76 
                                           89******************988.6888888888666666666554499************************ PP

                             TIGR00112  73 eevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelve 145
                                             v++ l++  ++++ l++Si+AGv+ e++e++l+++ +vvR+mPNt+a vg+g+ta++a+++vs++qk+ +e
  NCBI__GCF_000378965.1:WP_018232723.1  77 GGVARGLAGAVQARGPLVVSIAAGVRGEDIERWLGGDLPVVRCMPNTPALVGSGATALVANARVSSDQKAVAE 149
                                           *********9999************************************************************ PP

                             TIGR00112 146 ellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesge 217
                                           ++l+avG +v+++ e+ ldavtalsGSgPA+ fl++ea++dagv+lGLpre+a+ la qt  Gaakl  es+e
  NCBI__GCF_000378965.1:WP_018232723.1 150 SILRAVGLTVWLDdEAALDAVTALSGSGPAYCFLVMEAMEDAGVQLGLPRETARLLALQTAFGAAKLALESEE 222
                                           ************************************************************************* PP

                             TIGR00112 218 hpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263
                                           ++a+L+++Vts gGtT ++l+vLe +g+r+ +++a++aa +rs+eL
  NCBI__GCF_000378965.1:WP_018232723.1 223 DAATLRARVTSRGGTTEQALQVLESGGLRELLARALTAARDRSREL 268
                                           *******************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (275 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 16.66
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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