Alignments for a candidate for glpK in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Azospirillum brasilense Sp245

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate AZOBR_RS25905 AZOBR_RS25905 glycerol kinase

Query= reanno::Smeli:SM_b21009
         (497 letters)



>FitnessBrowser__azobra:AZOBR_RS25905
          Length = 501

 Score =  625 bits (1613), Expect = 0.0
 Identities = 301/492 (61%), Positives = 371/492 (75%), Gaps = 2/492 (0%)

Query: 3   GYILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVKEA 62
           G++LAIDQGTTSTRAIVFD     AGV ++EF QH+P  GWVEHDPE+IW+  V+ ++ A
Sbjct: 5   GHVLAIDQGTTSTRAIVFDRRGVPAGVARREFAQHYPADGWVEHDPEDIWRDTVAVMRGA 64

Query: 63  IEKSGITANDIAAIGITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLEKT 122
           ++++G++A DIAAIGITNQRET VVWDR TG+P+H AIVWQDRRT+  C KL ++G    
Sbjct: 65  VDEAGLSAADIAAIGITNQRETTVVWDRRTGEPVHRAIVWQDRRTSDLCRKLVEEGCGPL 124

Query: 123 FVKKTGLLLDPYFSGTKLNWLLSNVKGAQVRAAKGELCFGTIDTFLIWRLTGGECFCTDA 182
             +KTGLL+D YFS TK+ W+L +V GA+ RA +GELCFGTID+FL+ RLTGG    TDA
Sbjct: 125 VRRKTGLLIDSYFSATKIAWILDHVPGARERAERGELCFGTIDSFLLHRLTGGRVHATDA 184

Query: 183 TNASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGVTDPSLFGAAIPILGVAG 242
           TNASR+++++I    WDDEL  + R+P+ M+PEV D +A+FG T+P L G AIPI G+AG
Sbjct: 185 TNASRSMVFDIHRQDWDDELLALFRIPRAMMPEVLDSSAEFGATEPDLLGRAIPITGIAG 244

Query: 243 DQQAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGETTYALEG 302
           DQQAAT GQACF+PGM+KSTYGTGCFALLNTG + V S++ +LTT+AYRLDG TTYALEG
Sbjct: 245 DQQAATFGQACFQPGMVKSTYGTGCFALLNTGDEPVESRSNMLTTVAYRLDGRTTYALEG 304

Query: 303 SIFVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDPDARGAI 362
           SIF+AGAA++WLRDGL +I  A  T  +A     S  VYLVPAF GLGAPHWDP AR AI
Sbjct: 305 SIFIAGAAIKWLRDGLGIITHASQTDDMATRVPDSHGVYLVPAFVGLGAPHWDPQARAAI 364

Query: 363 FGMTRNTGPAEFARAALEAVCYQTRDLLEAMHKDW--RRNGNDTVLRVDGGMVASDWTMQ 420
           FG+T + GPA  ARAALEAV +QTRDL +AM  DW          LRVDGGM A+DW  Q
Sbjct: 365 FGLTLDAGPAHIARAALEAVAFQTRDLRDAMVSDWSAAHTATSDALRVDGGMAANDWLCQ 424

Query: 421 RLSDLLDAPVDRPVILETTALGVAWLAGSRAGVWPNQEAFAKSWARDRRFEPHMDEATRK 480
            L+D+LD PV+RP ++ETTALG A LAG + GV+ +Q A A +W  DRRFEP MD A R 
Sbjct: 425 FLADVLDLPVERPAVIETTALGAAGLAGLKVGVYRDQAALAGAWRCDRRFEPRMDAAKRV 484

Query: 481 VKLKGWRSAVKR 492
               GW  AV+R
Sbjct: 485 RLYDGWLDAVRR 496


Lambda     K      H
   0.319    0.134    0.415 

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: 838
Number of extensions: 26
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: 497
Length of database: 501
Length adjustment: 34
Effective length of query: 463
Effective length of database: 467
Effective search space:   216221
Effective search space used:   216221
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: 52 (24.6 bits)

Align candidate AZOBR_RS25905 AZOBR_RS25905 (glycerol kinase)
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.27537.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-213  695.1   0.0   2.3e-213  694.9   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS25905  AZOBR_RS25905 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS25905  AZOBR_RS25905 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  694.9   0.0  2.3e-213  2.3e-213       2     493 ..       6     497 ..       5     500 .. 0.98

  Alignments for each domain:
  == domain 1  score: 694.9 bits;  conditional E-value: 2.3e-213
                                 TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaee 70 
                                                ++aiDqGtts+raivfd++g   + a++e+ q++p +gwvEhdp++i++++v+v++ a+++++ +a++
  lcl|FitnessBrowser__azobra:AZOBR_RS25905   6 HVLAIDQGTTSTRAIVFDRRGVPAGVARREFAQHYPADGWVEHDPEDIWRDTVAVMRGAVDEAGLSAAD 74 
                                               589****************************************************************** PP

                                 TIGR01311  71 iaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlr 139
                                               iaaiGitnqREttvvWd++tg+p++ aivWqd+rt++++++l ee+    +r+ktGL++++YfsatK++
  lcl|FitnessBrowser__azobra:AZOBR_RS25905  75 IAAIGITNQRETTVVWDRRTGEPVHRAIVWQDRRTSDLCRKLVEEGCGPLVRRKTGLLIDSYFSATKIA 143
                                               ********************************************************************* PP

                                 TIGR01311 140 WlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipk 208
                                               W+ld+v+++r++ae+gel+fGt+d++l+++Ltgg+vh+td+tNASR +++++++++wd+ell+lf+ip+
  lcl|FitnessBrowser__azobra:AZOBR_RS25905 144 WILDHVPGARERAERGELCFGTIDSFLLHRLTGGRVHATDATNASRSMVFDIHRQDWDDELLALFRIPR 212
                                               ********************************************************************* PP

                                 TIGR01311 209 ellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkv 277
                                               +++Pe+ +ss+ +g +e++ ll++++pitg++Gdqqaa +gq+c+++g++K+tYgtGcF llntG+++v
  lcl|FitnessBrowser__azobra:AZOBR_RS25905 213 AMMPEVLDSSAEFGATEPD-LLGRAIPITGIAGDQQAATFGQACFQPGMVKSTYGTGCFALLNTGDEPV 280
                                               ******************9.************************************************* PP

                                 TIGR01311 278 iskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPa 346
                                                s++++Lttvay+l+g+++  yalEGs+++aGaa++wlrd l++i++a++++++a++v+ds+gvy+VPa
  lcl|FitnessBrowser__azobra:AZOBR_RS25905 281 ESRSNMLTTVAYRLDGRTT--YALEGSIFIAGAAIKWLRDGLGIITHASQTDDMATRVPDSHGVYLVPA 347
                                               ****************986..************************************************ PP

                                 TIGR01311 347 fsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamekdagvevk....vLkvDGgl 411
                                               f GL+aP+Wd++Ar++i+Glt ++  +hiaraaleavafq+rd+ +am +d  +  +    +L+vDGg+
  lcl|FitnessBrowser__azobra:AZOBR_RS25905 348 FVGLGAPHWDPQARAAIFGLTLDAGPAHIARAALEAVAFQTRDLRDAMVSDWSAAHTatsdALRVDGGM 416
                                               ***************************************************99544444559******* PP

                                 TIGR01311 412 sknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeere 480
                                               ++n++l+q+ ad+l+++verp v ettalGaA +agl+vgv++++  l+  ++ + ++fep+md+++r 
  lcl|FitnessBrowser__azobra:AZOBR_RS25905 417 AANDWLCQFLADVLDLPVERPAVIETTALGAAGLAGLKVGVYRDQAALAGAWRCD-RRFEPRMDAAKRV 484
                                               ******************************************************8.************* PP

                                 TIGR01311 481 kkykkwkeavers 493
                                               + y  w +av+r 
  lcl|FitnessBrowser__azobra:AZOBR_RS25905 485 RLYDGWLDAVRRV 497
                                               **********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (501 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.84
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources