GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpK in Xenophilus azovorans DSM 13620

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate WP_038210079.1 Q392_RS16455 glycerol kinase GlpK

Query= SwissProt::O66131
         (496 letters)



>NCBI__GCF_000745855.1:WP_038210079.1
          Length = 497

 Score =  558 bits (1437), Expect = e-163
 Identities = 278/495 (56%), Positives = 353/495 (71%), Gaps = 5/495 (1%)

Query: 4   YMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIASVL 63
           Y+LA+DQGT+SSR+I+F+  G IV MAQ+E  Q +PQPGWVEH+  EIW   LA    VL
Sbjct: 3   YLLALDQGTSSSRSIVFDAAGRIVAMAQRELPQIYPQPGWVEHDPMEIWQGQLATAREVL 62

Query: 64  SEAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYDPLF 123
           ++A++KP  +  IGITNQRETT+VWE+ TG P+++AIVWQ R+   +C +L+A G +   
Sbjct: 63  AKAKLKPTDIRAIGITNQRETTLVWERATGRPVHHAIVWQDRRAEPLCAKLRADGMEDTI 122

Query: 124 RKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVTDYS 183
           R+KTGL+IDAYFS TK+ W+LD+V G R RAERGEL FGT+D+WLIW+L+GG+VHVTD S
Sbjct: 123 REKTGLVIDAYFSATKLVWLLDNVPGLRARAERGELAFGTVDSWLIWQLTGGKVHVTDVS 182

Query: 184 NASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAGAAG 243
           NASRT++FN+H   WD +LL  L VP A++PEVRPSS  +A  A     G  +PI G AG
Sbjct: 183 NASRTMLFNVHRNAWDADLLAALKVPAALMPEVRPSSCHFA-DADAALLGAPLPIGGVAG 241

Query: 244 DQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDGKVEYALEG 303
           DQQAALFGQACF  GMAKNTYGTGCF+LM+TGEK   S++GLL T A     + +YA+EG
Sbjct: 242 DQQAALFGQACFGPGMAKNTYGTGCFLLMHTGEKFQPSRNGLLVTSAAQTSAQPQYAMEG 301

Query: 304 SIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSEVRGAV 363
           S+FV G+ +QWLRDGL+ I+ +   +  AE V    GV VVPAF GLG PYW ++ RG +
Sbjct: 302 SVFVGGAVVQWLRDGLQAIQGSGQVQALAESVPDAGGVMVVPAFTGLGAPYWKADARGTI 361

Query: 364 FGLTRGTTKEHFIRATLESLAYQTKDVLAVM----EADSGISLTTLRVDGGAVKNNFLMQ 419
            GLTRGTT  H  RA LES+AYQ+  +L  M    EA  G  +  LRVDGGA  N+ LMQ
Sbjct: 362 TGLTRGTTVAHIARAALESIAYQSAALLFAMSRDAEAAGGAPVAELRVDGGASVNDLLMQ 421

Query: 420 FQSDLLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRT 479
           FQ+DLL +PV RP V ETTALGAAYLAGLA G +   ++++ QW+ +RRF P M   +  
Sbjct: 422 FQADLLGIPVVRPEVVETTALGAAYLAGLACGVYAGTEELSRQWRAQRRFMPTMSRAQAD 481

Query: 480 MLYDGWKKAVRAAMA 494
                W+ AVR A A
Sbjct: 482 EAMARWEHAVRQATA 496


Lambda     K      H
   0.319    0.134    0.406 

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: 735
Number of extensions: 27
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: 496
Length of database: 497
Length adjustment: 34
Effective length of query: 462
Effective length of database: 463
Effective search space:   213906
Effective search space used:   213906
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_038210079.1 Q392_RS16455 (glycerol kinase GlpK)
to HMM TIGR01311 (glpK: glycerol kinase (EC 2.7.1.30))

# 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/TIGR01311.hmm
# target sequence database:        /tmp/gapView.170098.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01311  [M=496]
Accession:   TIGR01311
Description: glycerol_kin: glycerol kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     6e-215  700.1   0.1   6.7e-215  700.0   0.1    1.0  1  NCBI__GCF_000745855.1:WP_038210079.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038210079.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  700.0   0.1  6.7e-215  6.7e-215       2     493 ..       3     494 ..       2     497 .] 0.99

  Alignments for each domain:
  == domain 1  score: 700.0 bits;  conditional E-value: 6.7e-215
                             TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaai 74 
                                           +++a+DqGt+ssr ivfd+ g++va aq+el qi+p++gwvEhdp+ei++ ++++++e+l+k++ k+++i ai
  NCBI__GCF_000745855.1:WP_038210079.1   3 YLLALDQGTSSSRSIVFDAAGRIVAMAQRELPQIYPQPGWVEHDPMEIWQGQLATAREVLAKAKLKPTDIRAI 75 
                                           89*********************************************************************** PP

                             TIGR01311  75 GitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnvee 147
                                           GitnqREtt+vW+++tg+p+++aivWqd+r + ++++l++++ e+++rektGL++++YfsatKl Wlldnv++
  NCBI__GCF_000745855.1:WP_038210079.1  76 GITNQRETTLVWERATGRPVHHAIVWQDRRAEPLCAKLRADGMEDTIREKTGLVIDAYFSATKLVWLLDNVPG 148
                                           ************************************************************************* PP

                             TIGR01311 148 vrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssev 220
                                           +r++ae+gel fGtvd+wli++Ltggkvhvtdv+NASRt+l+n+++++wd +ll+++k+p++l+Pe+r+ss +
  NCBI__GCF_000745855.1:WP_038210079.1 149 LRARAERGELAFGTVDSWLIWQLTGGKVHVTDVSNASRTMLFNVHRNAWDADLLAALKVPAALMPEVRPSSCH 221
                                           ************************************************************************* PP

                             TIGR01311 221 ygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklgg 293
                                           +++ +++ ll++ +pi gv+Gdqqaal+gq+c+ +g+aKntYgtGcFll++tGek + s++glL t a +++ 
  NCBI__GCF_000745855.1:WP_038210079.1 222 FADADAA-LLGAPLPIGGVAGDQQAALFGQACFGPGMAKNTYGTGCFLLMHTGEKFQPSRNGLLVTSAAQTSA 293
                                           *****99.*************************************************************9998 PP

                             TIGR01311 294 kkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGl 366
                                           +   +ya+EGsv+v+Ga+vqwlrd l+ i+ + +v++la+sv+d +gv++VPaf+GL+aPyW++dArgti+Gl
  NCBI__GCF_000745855.1:WP_038210079.1 294 QP--QYAMEGSVFVGGAVVQWLRDGLQAIQGSGQVQALAESVPDAGGVMVVPAFTGLGAPYWKADARGTITGL 364
                                           76..6******************************************************************** PP

                             TIGR01311 367 trkttkehiaraaleavafqardileamekdag....vevkvLkvDGglsknnllmqiqadilgvkverpkva 435
                                           tr+tt +hiaraale++a+q+ ++l am++da+    + v++L+vDGg+s n+llmq+qad+lg++v+rp+v+
  NCBI__GCF_000745855.1:WP_038210079.1 365 TRGTTVAHIARAALESIAYQSAALLFAMSRDAEaaggAPVAELRVDGGASVNDLLMQFQADLLGIPVVRPEVV 437
                                           ********************************988888999******************************** PP

                             TIGR01311 436 ettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeavers 493
                                           ettalGaA++agla gv+  +eel+++++a+ ++f p+m++++ ++ +++w++av+++
  NCBI__GCF_000745855.1:WP_038210079.1 438 ETTALGAAYLAGLACGVYAGTEELSRQWRAQ-RRFMPTMSRAQADEAMARWEHAVRQA 494
                                           *****************************97.***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (497 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: 32.09
//
[ok]

This GapMind analysis is from Apr 09 2024. 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