Alignments for a candidate for sdaB in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Shewanella loihica PV-4

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 5209147 Shew_1625 L-serine dehydratase 1 (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5557
         (458 letters)



>FitnessBrowser__PV4:5209147
          Length = 458

 Score =  515 bits (1326), Expect = e-150
 Identities = 275/463 (59%), Positives = 338/463 (73%), Gaps = 13/463 (2%)

Query: 3   LSVFDLFKIGIGPSSSHTVGPMRAAARFAEGLRRDDLLNCTTSVKVELYGSLGATGKGHG 62
           +SVFD+FKIGIGPSSSHTVGPM+A   F + L +   L  T  ++ EL+GSLG TGKGHG
Sbjct: 2   ISVFDMFKIGIGPSSSHTVGPMKAGNIFIQDLEKHGHLAETDELRSELFGSLGQTGKGHG 61

Query: 63  SDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMIR-KPLA 121
           + KAV+LGL GE P+TVDT+ +DA L  +  +  L +     + F+ +  +   R K L 
Sbjct: 62  TGKAVILGLMGEAPETVDTDKIDATLAQVHDTQSLTMPNNKVVRFSREDGITYHRRKSLP 121

Query: 122 FHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLT------FPFK 175
            H N M   A+ A G  +  R YYSVGGGF++DE     + + +DA+P +      + F 
Sbjct: 122 AHANAMTLYAY-AKGNCIYQRTYYSVGGGFILDED----EILAQDASPASPIEAAPYDFN 176

Query: 176 SAKDLLGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPG 235
           SA +LL  C   GLSIS +M+ NE +   E E +  L  IWQ M+ CV  G + EGILPG
Sbjct: 177 SAAELLDMCVENGLSISALMMENELSIASEKEVKERLWTIWQTMKSCVERGYQKEGILPG 236

Query: 236 GLKVKRRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAG 295
           GLK++RRA AL+R+L K     + DPL+ +DWV+L+ALAVNE+NA G RVVTAPTNGAAG
Sbjct: 237 GLKLRRRAPALYRRL-KAESKTVVDPLTAMDWVDLFALAVNEQNAAGDRVVTAPTNGAAG 295

Query: 296 IIPAVLHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAA 355
           IIPAVL YY  F+     D   ++LLTAAAIGILYK+NASISGAEVGCQGEVGVACSMAA
Sbjct: 296 IIPAVLCYYDTFVQEVDLDICCQYLLTAAAIGILYKKNASISGAEVGCQGEVGVACSMAA 355

Query: 356 GALCEVLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAM 415
            AL E++GG+V+ VENAAEIGMEHNLGLTCDP+GGLVQVPCIERNAMG+VKAINA R+AM
Sbjct: 356 AALTEIMGGTVEHVENAAEIGMEHNLGLTCDPVGGLVQVPCIERNAMGAVKAINASRLAM 415

Query: 416 RGDGHHFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458
           RGDG+H VSLDKVI+TM  TG DM+SKYKETA+GGLAVNI+EC
Sbjct: 416 RGDGNHKVSLDKVIKTMMDTGKDMRSKYKETAKGGLAVNIVEC 458


Lambda     K      H
   0.320    0.136    0.401 

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: 654
Number of extensions: 18
Number of successful extensions: 4
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: 458
Length of database: 458
Length adjustment: 33
Effective length of query: 425
Effective length of database: 425
Effective search space:   180625
Effective search space used:   180625
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 5209147 Shew_1625 (L-serine dehydratase 1 (RefSeq))
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.5759.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.2e-216  705.9   1.9   1.3e-216  705.7   1.9    1.0  1  lcl|FitnessBrowser__PV4:5209147  Shew_1625 L-serine dehydratase 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209147  Shew_1625 L-serine dehydratase 1 (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  705.7   1.9  1.3e-216  1.3e-216       1     450 []       2     455 ..       2     455 .. 0.99

  Alignments for each domain:
  == domain 1  score: 705.7 bits;  conditional E-value: 1.3e-216
                        TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpeevd 78 
                                      isvfd+fkiGiGPssshtvGPmka++ f+++l+k+g+l+++++++ +l+Gsl+ tGkGh+t kav+lGl+Ge pe+vd
  lcl|FitnessBrowser__PV4:5209147   2 ISVFDMFKIGIGPSSSHTVGPMKAGNIFIQDLEKHGHLAETDELRSELFGSLGQTGKGHGTGKAVILGLMGEAPETVD 79 
                                      79**************************************************************************** PP

                        TIGR00720  79 iesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevlkektyysvGGGfivdeee 155
                                      +++i++ l++v+++++l++ n+k ++f++e+ ++++ +++lp h+n+++l ay++  + ++++tyysvGGGfi+de+e
  lcl|FitnessBrowser__PV4:5209147  80 TDKIDATLAQVHDTQSLTMPNNKVVRFSREDGITYHrRKSLPAHANAMTLYAYAKG-NCIYQRTYYSVGGGFILDEDE 156
                                      ************************************999**************988.9*******************9 PP

                        TIGR00720 156 lkkeeeeee....evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeecierglkaegvl 229
                                      +  ++++ +     +py+f+saaell++C e+glsis++++ene +++se+ev+++l +iw++m++c+erg ++eg+l
  lcl|FitnessBrowser__PV4:5209147 157 ILAQDASPAspieAAPYDFNSAAELLDMCVENGLSISALMMENELSIASEKEVKERLWTIWQTMKSCVERGYQKEGIL 234
                                      987777666577789*************************************************************** PP

                        TIGR00720 230 pGglkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeas 307
                                      pGglk++rra++l+r+lka+++t  dpl+++dwv l+alavne+naaG+rvvtaPtnGaagiiPavl yy++fv+e+ 
  lcl|FitnessBrowser__PV4:5209147 235 PGGLKLRRRAPALYRRLKAESKTVVDPLTAMDWVDLFALAVNEQNAAGDRVVTAPTNGAAGIIPAVLCYYDTFVQEVD 312
                                      ****************************************************************************** PP

                        TIGR00720 308 eekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgG 385
                                       ++  ++llta+aiGilyk+nasisgaevGCqgevGvacsmaaa+l+e++ggt+e venaaei+mehnlGltCdPvgG
  lcl|FitnessBrowser__PV4:5209147 313 LDICCQYLLTAAAIGILYKKNASISGAEVGCQGEVGVACSMAAAALTEIMGGTVEHVENAAEIGMEHNLGLTCDPVGG 390
                                      ****************************************************************************** PP

                        TIGR00720 386 lvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                      lvq+PCierna++avkaina+rla+++dg++kvsldkvi+tm++tGkdm++kyket+kgGlav++
  lcl|FitnessBrowser__PV4:5209147 391 LVQVPCIERNAMGAVKAINASRLAMRGDGNHKVSLDKVIKTMMDTGKDMRSKYKETAKGGLAVNI 455
                                      ***************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (458 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: 10.28
//
[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