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 5208228 Shew_0740 L-serine dehydratase 1 (RefSeq)

Query= BRENDA::P16095
         (454 letters)



>FitnessBrowser__PV4:5208228
          Length = 455

 Score =  645 bits (1664), Expect = 0.0
 Identities = 328/451 (72%), Positives = 366/451 (81%), Gaps = 1/451 (0%)

Query: 1   MISLFDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLLDSVTRVAVDVYGSLSLTGKGH 60
           M+S FD+FK+G+GPSSSHTVGPMKA K FVDDL ++G L S+T V VD+YGSLSLTGKGH
Sbjct: 1   MVSAFDIFKIGVGPSSSHTVGPMKAAKGFVDDLRQRGELLSITSVKVDIYGSLSLTGKGH 60

Query: 61  HTDIAIIMGLAGNEPATVDIDSIPGFIRDVEERERLLLAQGRHEVDFPRDNGMRFHNGNL 120
           HTD AIIMGLAGN P TVDID  P FIR V     L L    H VDFP +  + FH   L
Sbjct: 61  HTDSAIIMGLAGNSPETVDIDLTPEFIRQVAMTSCLPLGTEGHGVDFPPE-AVVFHPEAL 119

Query: 121 PLHENGMQIHAYNGDEVVYSKTYYSIGGGFIVDEEHFGQDAANEVSVPYPFKSATELLAY 180
            LHENGM + AY G + VY KTYYSIGGGFIVDEEHFG  AANEV +PYPF +A ELL  
Sbjct: 120 ALHENGMTLSAYVGQQCVYHKTYYSIGGGFIVDEEHFGMTAANEVVLPYPFANAEELLDL 179

Query: 181 CNETGYSLSGLAMQNELALHSKKEIDEYFAHVWQTMQACIDRGMNTEGVLPGPLRVPRRA 240
           C ETG S+S + M NE ALHS+  I E F  VW TM+  I+RG +TEGVL GPLRVPRRA
Sbjct: 180 CQETGMSISAIMMANERALHSEAHIAEGFEAVWHTMKEAIERGCHTEGVLAGPLRVPRRA 239

Query: 241 SALRRMLVSSDKLSNDPMNVIDWVNMFALAVNEENAAGGRVVTAPTNGACGIVPAVLAYY 300
            AL R L + ++LS DPM ++DWVNMFALAV+EENAAGGRVVT+PTNGA GI+PAVLAY+
Sbjct: 240 PALFRQLATGERLSADPMMIVDWVNMFALAVSEENAAGGRVVTSPTNGAAGIIPAVLAYF 299

Query: 301 DHFIESVSPDIYTRYFMAAGAIGALYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGG 360
           D FI+ V P  Y+RYF+AA AIG LYK NASISGAEVGCQGEVGVACSMAAAGLAEL+GG
Sbjct: 300 DKFIQPVGPKEYSRYFLAAAAIGGLYKRNASISGAEVGCQGEVGVACSMAAAGLAELMGG 359

Query: 361 SPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINAARMALRRTSAPRVS 420
           +P QVC+AAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAIN+ARMALRR S PRVS
Sbjct: 360 NPAQVCIAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINSARMALRRNSEPRVS 419

Query: 421 LDKVIETMYETGKDMNAKYRETSRGGLAIKV 451
           LDKVI TMYETGKDM+ KYRETS+GGLAIKV
Sbjct: 420 LDKVIATMYETGKDMHVKYRETSQGGLAIKV 450


Lambda     K      H
   0.318    0.135    0.396 

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: 669
Number of extensions: 25
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: 454
Length of database: 455
Length adjustment: 33
Effective length of query: 421
Effective length of database: 422
Effective search space:   177662
Effective search space used:   177662
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 5208228 Shew_0740 (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.25462.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   6.7e-218  710.0   0.7   7.6e-218  709.8   0.7    1.0  1  lcl|FitnessBrowser__PV4:5208228  Shew_0740 L-serine dehydratase 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208228  Shew_0740 L-serine dehydratase 1 (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  709.8   0.7  7.6e-218  7.6e-218       1     450 []       2     450 ..       2     450 .. 0.99

  Alignments for each domain:
  == domain 1  score: 709.8 bits;  conditional E-value: 7.6e-218
                        TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpeevd 78 
                                      +s fd+fkiG+GPssshtvGPmkaak fv++l+++g+l ++++vkvd+yGsl+ltGkGh+td+a+++Gl+G++pe+vd
  lcl|FitnessBrowser__PV4:5208228   2 VSAFDIFKIGVGPSSSHTVGPMKAAKGFVDDLRQRGELLSITSVKVDIYGSLSLTGKGHHTDSAIIMGLAGNSPETVD 79 
                                      699*************************************************************************** PP

                        TIGR00720  79 iesieklleeveeekklkla.nqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGGGfivdeee 155
                                      i+ +++++++v+ ++ l l+ + + ++f   + ++f+ e+l lheng++l+ay ++ + +++ktyys+GGGfivdee+
  lcl|FitnessBrowser__PV4:5208228  80 IDLTPEFIRQVAMTSCLPLGtEGHGVDFP-PEAVVFHPEALALHENGMTLSAYVGQ-QCVYHKTYYSIGGGFIVDEEH 155
                                      *******************978899***9.6789********************99.99******************* PP

                        TIGR00720 156 lkkeeeeeeevpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeecierglkaegvlpGgl 233
                                      ++ ++++e+ +pypf +a+ell+lC+e+g+sis+++++ne al+se+++ + + ++w++m+e+ierg+++egvl+G+l
  lcl|FitnessBrowser__PV4:5208228 156 FGMTAANEVVLPYPFANAEELLDLCQETGMSISAIMMANERALHSEAHIAEGFEAVWHTMKEAIERGCHTEGVLAGPL 233
                                      ****************************************************************************** PP

                        TIGR00720 234 kvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekv 311
                                      +v+rra++l r+l + e+ s+dp++++dwvn++alav+eenaaGgrvvt+PtnGaagiiPavlay++kf++ +  +++
  lcl|FitnessBrowser__PV4:5208228 234 RVPRRAPALFRQLATGERLSADPMMIVDWVNMFALAVSEENAAGGRVVTSPTNGAAGIIPAVLAYFDKFIQPVGPKEY 311
                                      ****************************************************************************** PP

                        TIGR00720 312 vrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqi 389
                                       r++l+a+aiG lyk+nasisgaevGCqgevGvacsmaaaglael+gg+p qv++aaei+mehnlGltCdPv+G+vq+
  lcl|FitnessBrowser__PV4:5208228 312 SRYFLAAAAIGGLYKRNASISGAEVGCQGEVGVACSMAAAGLAELMGGNPAQVCIAAEIGMEHNLGLTCDPVAGQVQV 389
                                      ****************************************************************************** PP

                        TIGR00720 390 PCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                      PCiernaia+vkain+ar+al+++++++vsldkvi+tm+etGkdm+ ky+ets+gGla+kv
  lcl|FitnessBrowser__PV4:5208228 390 PCIERNAIASVKAINSARMALRRNSEPRVSLDKVIATMYETGKDMHVKYRETSQGGLAIKV 450
                                      ***********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (455 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: 6.90
//
[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