Alignments for a candidate for sdaB in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Bacteroides thetaiotaomicron VPI-5482

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 354204 BT4678 L-serine dehydratase (NCBI ptt file)

Query= reanno::acidovorax_3H11:Ac3H11_929
         (466 letters)



>FitnessBrowser__Btheta:354204
          Length = 411

 Score =  298 bits (762), Expect = 3e-85
 Identities = 190/459 (41%), Positives = 252/459 (54%), Gaps = 67/459 (14%)

Query: 4   SVFDLFKIGIGPSSSHTVGPMIAARQFACHVQGTLGLDAVHHVTVELFGSLSATGVGHGT 63
           S+ +L++IG GPSSSHT+GP  AA  F                 V L+GSL+ATG GH T
Sbjct: 12  SIKELYRIGTGPSSSHTMGPRKAAEMFVERHPDAASFK------VTLYGSLAATGKGHMT 65

Query: 64  DKAVLLGLAGHEPDHIDPDQILPAIADIRTRQTLALLGEHPVPFVEKEHLLFRRKSLPLH 123
           D A++             D + PA                PV  V +  +      LP H
Sbjct: 66  DVAII-------------DTLQPAA---------------PVEIVWQPKVF-----LPFH 92

Query: 124 PNGMAFHAFDAQGNEIATREYYSVGGGFVIDAAGERVLNSAATAGPDAVGHAQGLPHPFR 183
           PNGM F A DA    +     YS+GGG + +      + S    G + +           
Sbjct: 93  PNGMTFAALDADNKILENWTVYSIGGGALAENNDNPTIESPEVYGMNNM----------- 141

Query: 184 TGAELLAQCQATGLTPAQLM--AANEQHWRSASEVRRQLMAIWKTMAGAVQRGCASTGTL 241
              E+L  C+ TG +  + +    NE  W   +EV       W TM  A+ RG  + G L
Sbjct: 142 --TEILQWCERTGKSYWEYVKECENEDIWDYLAEV-------WDTMKDAIHRGLEAEGVL 192

Query: 242 PGPMHVRRRAAELHHKLSSAPEAALRDPLSMLDWVNLYAMAVNEENAAGGRVVTAPTNGA 301
           PGP+++RR+A+  + + +   ++     L     V  YA+AV+EENA+GG++VTAPT G+
Sbjct: 193 PGPLNLRRKASTYYIRATGYKQS-----LQSRGLVFSYALAVSEENASGGKIVTAPTCGS 247

Query: 302 AGVIPAVLHYYVNFLPGANEDGIATFLLTAGAIGIIYKENASLSGAEVGCQGEVGVACSM 361
            GV+PAVL Y++      ++  I   L TAG IG I K NAS+SGAEVGCQGEVGVAC+M
Sbjct: 248 CGVMPAVL-YHLQKSRDFSDMRILRALATAGLIGNIVKFNASISGAEVGCQGEVGVACAM 306

Query: 362 AAGALAAVMGGSPEQIENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAIKAINAARM 421
           A+ A   + GGSP QIE AAE+G+EH+LGMTCDPV GLVQIPCIERNA  A +A++A   
Sbjct: 307 ASAAANQLFGGSPAQIEYAAEMGLEHHLGMTCDPVCGLVQIPCIERNAYAAARALDANLY 366

Query: 422 ALRGDGQHVVSLDKVIKTMMQTGADMKVKYKETSRGGLA 460
           +   DG H VS DKV++ M QTG D+   YKETS GGLA
Sbjct: 367 SAFTDGMHRVSFDKVVQVMKQTGHDLPSLYKETSEGGLA 405


Lambda     K      H
   0.319    0.134    0.398 

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: 521
Number of extensions: 32
Number of successful extensions: 6
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: 466
Length of database: 411
Length adjustment: 32
Effective length of query: 434
Effective length of database: 379
Effective search space:   164486
Effective search space used:   164486
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: 51 (24.3 bits)

Align candidate 354204 BT4678 (L-serine dehydratase (NCBI ptt file))
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

# 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/TIGR00720.hmm
# target sequence database:        /tmp/gapView.4609.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00720  [M=450]
Accession:   TIGR00720
Description: sda_mono: L-serine ammonia-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.1e-131  425.8   0.7   7.3e-112  360.4   0.1    2.0  2  lcl|FitnessBrowser__Btheta:354204  BT4678 L-serine dehydratase (NCB


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:354204  BT4678 L-serine dehydratase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   3.5e-22   3.5e-22       2      77 ..      12      81 ..      11      86 .. 0.91
   2 !  360.4   0.1  7.3e-112  7.3e-112     114     448 ..      84     406 ..      76     408 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 3.5e-22
                          TIGR00720  2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpeev 77
                                       s+ +l++iG GPsssht+GP kaa++fve+  ++      ++ kv+lyGsla+tGkGh td a++  l+   p e+
  lcl|FitnessBrowser__Btheta:354204 12 SIKELYRIGTGPSSSHTMGPRKAAEMFVERHPDA------ASFKVTLYGSLAATGKGHMTDVAIIDTLQPAAPVEI 81
                                       7889************************998655......899**********************99988877665 PP

  == domain 2  score: 360.4 bits;  conditional E-value: 7.3e-112
                          TIGR00720 114 k.devlplhenglrlkaydeegevlkektyysvGGGfivdeeelkkeeeeeeevpypfksaaellelCkeeglsis 188
                                        + + +lp+h+ng+++ a+d ++++l + t ys+GGG + ++++     + e+   y  ++++e+l+ C+++g+s  
  lcl|FitnessBrowser__Btheta:354204  84 QpKVFLPFHPNGMTFAALDADNKILENWTVYSIGGGALAENNDN---PTIESPEVYGMNNMTEILQWCERTGKSYW 156
                                        546789******************************99776544...44555667********************9 PP

                          TIGR00720 189 evvlenekalrseeevraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeetskdplavldwvn 264
                                        e v e e     +e++ ++l+e+w++m+++i+rgl+aegvlpG+l+++r+a++ + + +  +++    l+    v 
  lcl|FitnessBrowser__Btheta:354204 157 EYVKECE-----NEDIWDYLAEVWDTMKDAIHRGLEAEGVLPGPLNLRRKASTYYIRATGYKQS----LQSRGLVF 223
                                        9998766.....47899************************************99887665555....67778999 PP

                          TIGR00720 265 lyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqg 340
                                         yalav+eena+Gg++vtaPt G++g++Pavl++  +  ++ s+ ++ r l tag iG + k nasisgaevGCqg
  lcl|FitnessBrowser__Btheta:354204 224 SYALAVSEENASGGKIVTAPTCGSCGVMPAVLYH-LQKSRDFSDMRILRALATAGLIGNIVKFNASISGAEVGCQG 298
                                        9******************************955.5568899********************************** PP

                          TIGR00720 341 evGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkk 416
                                        evGvac+ma+a+  +l+gg+p q+e aae+++eh+lG+tCdPv GlvqiPCierna aa +a++a   +   dg +
  lcl|FitnessBrowser__Btheta:354204 299 EVGVACAMASAAANQLFGGSPAQIEYAAEMGLEHHLGMTCDPVCGLVQIPCIERNAYAAARALDANLYSAFTDGMH 374
                                        **************************************************************************** PP

                          TIGR00720 417 kvsldkvietmretGkdmkakyketskgGlav 448
                                        +vs+dkv+++m++tG+d+ + ykets+gGla+
  lcl|FitnessBrowser__Btheta:354204 375 RVSFDKVVQVMKQTGHDLPSLYKETSEGGLAK 406
                                        ******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (411 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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 2.48
//
[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:

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