GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PRO3 in Pseudomonas fluorescens FW300-N2C3

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate AO356_13420 AO356_13420 pyrroline-5-carboxylate reductase

Query= SwissProt::P22008
         (273 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_13420
          Length = 272

 Score =  385 bits (988), Expect = e-112
 Identities = 200/273 (73%), Positives = 233/273 (85%), Gaps = 1/273 (0%)

Query: 1   MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60
           MS  RIAFIGAGNMAASLIGGLRA+G+ A+ IRASDPG E R +++ E  I+    NA+A
Sbjct: 1   MSNTRIAFIGAGNMAASLIGGLRAKGLDASLIRASDPGEETRTRVSAEHGIETFADNAQA 60

Query: 61  VADADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMP 120
           +  ADV+VL+VKPQAMK VC+AL P+LKP QL+VSIAAGI CAS+  WLG+ +P+VRCMP
Sbjct: 61  IDGADVIVLAVKPQAMKTVCEALRPSLKPHQLVVSIAAGITCASMNNWLGE-QPIVRCMP 119

Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180
           NTPALLRQG SGL+A   VSA Q +QA  LLSAVG+ALWLD E Q+DAVTAVSGSGPAYF
Sbjct: 120 NTPALLRQGVSGLFATPHVSAEQRQQAETLLSAVGLALWLDTEQQLDAVTAVSGSGPAYF 179

Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAA 240
           FLL++AMT AGEKLGL+RETA++LTLQTALGAA MA+SS+V+ AELRRRVTSP GTTEAA
Sbjct: 180 FLLIEAMTAAGEKLGLTRETAAQLTLQTALGAAHMAVSSDVDAAELRRRVTSPAGTTEAA 239

Query: 241 IKSFQANGFEALVEQALNAASQRSAELAEQLGQ 273
           IKSFQA GFEALVE+AL AA+ RSAE+AEQLGQ
Sbjct: 240 IKSFQAGGFEALVEKALGAAAHRSAEMAEQLGQ 272


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: 269
Number of extensions: 6
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: 272
Length adjustment: 25
Effective length of query: 248
Effective length of database: 247
Effective search space:    61256
Effective search space used:    61256
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 AO356_13420 AO356_13420 (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.27275.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
    6.5e-81  257.8   6.2    7.4e-81  257.6   6.2    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13420  AO356_13420 pyrroline-5-carboxyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13420  AO356_13420 pyrroline-5-carboxylate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.6   6.2   7.4e-81   7.4e-81       1     263 []       6     266 ..       6     266 .. 0.97

  Alignments for each domain:
  == domain 1  score: 257.6 bits;  conditional E-value: 7.4e-81
                                       TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvv 63 
                                                     ia+iGaGnm+++l+ gl +kg   ++ i   ++ ee +++  +e g+e+ +d+++a++ adv+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13420   6 IAFIGAGNMAASLIGGLRAKGLD-ASLIRASDPGEETRTRVSAEHGIETFADNAQAIDGADVI 67 
                                                     89**************9999765.7888888889***************************** PP

                                       TIGR00112  64 llavKPqdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgag 126
                                                     +lavKPq +++v++ l+  + + ++l++Si+AG+t++ ++++l+ e+++vR+mPNt+a +++g
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13420  68 VLAVKPQAMKTVCEALRP-SLKPHQLVVSIAAGITCASMNNWLG-EQPIVRCMPNTPALLRQG 128
                                                     *****************9.6669********************7.699*************** PP

                                       TIGR00112 127 vtaiaassevseeqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagv 188
                                                     v++++a+ +vs+eq++++e ll+avG +++++ e++ldavta+sGSgPA++flliea+ +ag 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13420 129 VSGLFATPHVSAEQRQQAETLLSAVGLALWLDtEQQLDAVTAVSGSGPAYFFLLIEAMTAAGE 191
                                                     *************************************************************** PP

                                       TIGR00112 189 klGLpreeakelaaqtlkGaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavie 251
                                                     klGL+re+a +l+ qt  Gaa++   s+ ++a+L+ +VtsP+GtT a++++++++g+++ v++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13420 192 KLGLTRETAAQLTLQTALGAAHMAVSSDVDAAELRRRVTSPAGTTEAAIKSFQAGGFEALVEK 254
                                                     *************************************************************** PP

                                       TIGR00112 252 aveaavkrseeL 263
                                                     a+ aa++rs e+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13420 255 ALGAAAHRSAEM 266
                                                     ********9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (272 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: 7.75
//
[ok]

This GapMind analysis is from Sep 17 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