Alignments for a candidate for kbl in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for kbl in Pedobacter sp. GW460-11-11-14-LB5

Align 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29) (characterized)
to candidate CA265_RS15280 CA265_RS15280 glycine C-acetyltransferase

Query= reanno::Cup4G11:RR42_RS28295
         (400 letters)



>FitnessBrowser__Pedo557:CA265_RS15280
          Length = 395

 Score =  527 bits (1358), Expect = e-154
 Identities = 249/389 (64%), Positives = 322/389 (82%), Gaps = 2/389 (0%)

Query: 11  IRQELESIEQAGLFKTERVIASPQGSLIRTTDGKEVINLCANNYLGLSSHPEVVEAAHRA 70
           +++ELE IE AGLFK ER+I +PQG+ I+ + G EV+N CANNYLGLSSHP+V+EAA +A
Sbjct: 9   LQKELEEIENAGLFKRERIIITPQGADIKVSGGAEVVNFCANNYLGLSSHPKVIEAAKKA 68

Query: 71  LGERGFGLSSVRFICGTQDLHKSLEARLASFLGTEDTILYGSAFDANGGLFETLLGSDDA 130
           + + G+G+SSVRFICGTQD+HK LEA+++ FLGTEDTILY +AFDANGG+FE L  ++DA
Sbjct: 69  IDDHGYGMSSVRFICGTQDVHKELEAKISKFLGTEDTILYAAAFDANGGVFEPLFNAEDA 128

Query: 131 VISDELNHASIIDGIRLCKAKRFRYKNNDLEDLREQLKAADAAGARFKLVFTDGVFSMDG 190
           +ISDELNHASIIDG+RLCKA+RFRYKN D+EDL +QL AA     R +++ TDG FSMDG
Sbjct: 129 IISDELNHASIIDGVRLCKAQRFRYKNADMEDLEKQLIAAK--DCRHRIIVTDGAFSMDG 186

Query: 191 TIARLDEIREICDEFGALLGIDECHATGFLGQRGRGSHEHRGIFGKVDIITGTLGKALGG 250
           ++A LD+I ++ D++ AL+ IDE H TGF+G+ GRG+HEH  +  ++DIITGTLGKALGG
Sbjct: 187 SVAPLDKIADLADKYEALIMIDESHCTGFIGKNGRGTHEHFNVIDRIDIITGTLGKALGG 246

Query: 251 ASGGFTSGRKEVVALLRQRSRPYLFSNTVAPCIVGATLKVLDLLEADTTLRDKLERNARY 310
           ASGGFTSG+KE++ +LRQRSRPYLFSNT+AP I GA++ VLD+L   T+LRDKLE N +Y
Sbjct: 247 ASGGFTSGKKEIIDMLRQRSRPYLFSNTLAPAIAGASIAVLDMLSETTSLRDKLENNTKY 306

Query: 311 FRGKLGTLGFDVKPGDHPIIPVMVYDAEKAQRLSRRLLELGVYVIGFFYPVVPRGQARIR 370
           FR K+   GFD+KPG HPI+PVM+YDA+ AQ+ + ++LE G+YVIGFFYPVVP+G+ARIR
Sbjct: 307 FREKMTEAGFDIKPGFHPIVPVMLYDAKIAQQFAAKMLEEGIYVIGFFYPVVPQGKARIR 366

Query: 371 VQISALHDSAELDQALEAFEIAGKELGII 399
           VQ+SA H+   LD+A+ AF   GKELG+I
Sbjct: 367 VQLSAGHEQHHLDKAIAAFTKVGKELGVI 395


Lambda     K      H
   0.321    0.140    0.402 

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: 544
Number of extensions: 16
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: 400
Length of database: 395
Length adjustment: 31
Effective length of query: 369
Effective length of database: 364
Effective search space:   134316
Effective search space used:   134316
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: 50 (23.9 bits)

Align candidate CA265_RS15280 CA265_RS15280 (glycine C-acetyltransferase)
to HMM TIGR01822 (kbl: glycine C-acetyltransferase (EC 2.3.1.29))

# 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/TIGR01822.hmm
# target sequence database:        /tmp/gapView.17521.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01822  [M=393]
Accession:   TIGR01822
Description: 2am3keto_CoA: glycine C-acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.7e-213  694.7   0.9   1.9e-213  694.5   0.9    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS15280  CA265_RS15280 glycine C-acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15280  CA265_RS15280 glycine C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  694.5   0.9  1.9e-213  1.9e-213       3     393 .]       7     395 .]       5     395 .] 0.99

  Alignments for each domain:
  == domain 1  score: 694.5 bits;  conditional E-value: 1.9e-213
                                  TIGR01822   3 ailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGf 70 
                                                 +l++ele i++aGlfk+erii++pq+adi+v+ G ev+nfcannylGls+hp+vi+aak+a+d+hG+
  lcl|FitnessBrowser__Pedo557:CA265_RS15280   7 PVLQKELEEIENAGLFKRERIIITPQGADIKVSGGAEVVNFCANNYLGLSSHPKVIEAAKKAIDDHGY 74 
                                                57899*************************************************************** PP

                                  TIGR01822  71 GlssvrficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidG 138
                                                G+ssvrficGtqd+hkele+k+++flgted+ilya++fdangG+fe+l+ +edaiisd+lnhasiidG
  lcl|FitnessBrowser__Pedo557:CA265_RS15280  75 GMSSVRFICGTQDVHKELEAKISKFLGTEDTILYAAAFDANGGVFEPLFNAEDAIISDELNHASIIDG 142
                                                ******************************************************************** PP

                                  TIGR01822 139 vrlckakryryenadledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvd 206
                                                vrlcka+r+ry+nad+edle++l +a++  +r+r+i+tdG+fsmdG++apld+i++la+ky+al+++d
  lcl|FitnessBrowser__Pedo557:CA265_RS15280 143 VRLCKAQRFRYKNADMEDLEKQLIAAKD--CRHRIIVTDGAFSMDGSVAPLDKIADLADKYEALIMID 208
                                                ***********************98875..6************************************* PP

                                  TIGR01822 207 echatGflGatGrGsaelldvldkvdiitgtlGkalGGasGGfttakkevvellrqrsrpylfsnsla 274
                                                e+h+tGf+G++GrG++e ++v+d++diitgtlGkalGGasGGft++kke++++lrqrsrpylfsn+la
  lcl|FitnessBrowser__Pedo557:CA265_RS15280 209 ESHCTGFIGKNGRGTHEHFNVIDRIDIITGTLGKALGGASGGFTSGKKEIIDMLRQRSRPYLFSNTLA 276
                                                ******************************************************************** PP

                                  TIGR01822 275 pavvgasikvlelleasnelrdklventryfrekleaaGfdvkpaehaiipvmlydaklaqklaerll 342
                                                pa+ gasi+vl++l++++ lrdkl++nt+yfrek++ aGfd+kp+ h+i+pvmlydak+aq++a+++l
  lcl|FitnessBrowser__Pedo557:CA265_RS15280 277 PAIAGASIAVLDMLSETTSLRDKLENNTKYFREKMTEAGFDIKPGFHPIVPVMLYDAKIAQQFAAKML 344
                                                ******************************************************************** PP

                                  TIGR01822 343 eeGiyviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                                eeGiyviGffypvvp+G+arirvqlsa+he+++ldka+ af+kvG+elgvi
  lcl|FitnessBrowser__Pedo557:CA265_RS15280 345 EEGIYVIGFFYPVVPQGKARIRVQLSAGHEQHHLDKAIAAFTKVGKELGVI 395
                                                *************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (395 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: 7.58
//
[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