Alignments for a candidate for sdaB in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Shewanella oneidensis MR-1

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 201398 SO2248 L-serine dehydratase 1 (NCBI ptt file)

Query= BRENDA::P16095
         (454 letters)



>FitnessBrowser__MR1:201398
          Length = 458

 Score =  515 bits (1327), Expect = e-150
 Identities = 256/456 (56%), Positives = 333/456 (73%), Gaps = 6/456 (1%)

Query: 1   MISLFDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLLDSVTRVAVDVYGSLSLTGKGH 60
           MIS+FDMFK+GIGPSSSHTVGPMKAGK F+  L + G +  +  +  +++GSL  TGKGH
Sbjct: 1   MISVFDMFKIGIGPSSSHTVGPMKAGKIFMQHLADSGQIGQIDELRAELFGSLGQTGKGH 60

Query: 61  HTDIAIIMGLAGNEPATVDIDSIPGFIRDVEERERLLLAQGRHEVDFPRDNGMRFHNG-N 119
            T  A+I+GL G +P TVD DSI G +  V + E L ++ G+  V F R++G+ +H   +
Sbjct: 61  GTGKAVILGLMGEDPETVDTDSIDGILEHVSKSETLTISCGK-VVKFTREDGITYHRRKS 119

Query: 120 LPLHENGMQIHAYNGDEVVYSKTYYSIGGGFIVDEEHFGQDAANEVS----VPYPFKSAT 175
           LP H N M ++AY+  E ++ +TYYS+GGGFI+DE+   Q  A+  S     PY F S+ 
Sbjct: 120 LPAHANAMTLYAYSKGECIFERTYYSVGGGFILDEDEINQRNASPASQIESAPYDFNSSA 179

Query: 176 ELLAYCNETGYSLSGLAMQNELALHSKKEIDEYFAHVWQTMQACIDRGMNTEGVLPGPLR 235
           +LL  C E G S+S L M NEL+L S++E+     ++WQTM+ CI+RG   EG+LPG L+
Sbjct: 180 QLLELCTEHGLSISSLMMANELSLASEEEVKAKLWNIWQTMKTCIERGYQKEGILPGGLK 239

Query: 236 VPRRASALRRMLVSSDKLSNDPMNVIDWVNMFALAVNEENAAGGRVVTAPTNGACGIVPA 295
           + RRA AL R L +  + + DP+  +DWV++FAL+VNE+NAAG RVVTAPTNGA GI+PA
Sbjct: 240 LRRRAPALYRRLKAEGRNNVDPLTAMDWVDLFALSVNEQNAAGDRVVTAPTNGAAGIIPA 299

Query: 296 VLAYYDHFIESVSPDIYTRYFMAAGAIGALYKMNASISGAEVGCQGEVGVACSMAAAGLA 355
           VL YYD F++ V  D+  RY + A AIG LYK NASISGAEVGCQGEVGVACSMAA  L 
Sbjct: 300 VLCYYDTFVQEVDIDVCARYLLTAAAIGILYKKNASISGAEVGCQGEVGVACSMAAGALT 359

Query: 356 ELLGGSPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINAARMALRRTS 415
           E++GG+ E V  AAEIGMEHNLGLTCDPV G VQVPCIERNA+ ++KAINA+RMALR   
Sbjct: 360 EIMGGTVEHVENAAEIGMEHNLGLTCDPVGGLVQVPCIERNAMGAIKAINASRMALRGDG 419

Query: 416 APRVSLDKVIETMYETGKDMNAKYRETSRGGLAIKV 451
             +VSLDKVI+TM +TGKDM +KY+ET++GGLA+ +
Sbjct: 420 NHKVSLDKVIKTMMDTGKDMRSKYKETAKGGLAVNI 455


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: 629
Number of extensions: 26
Number of successful extensions: 3
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: 458
Length adjustment: 33
Effective length of query: 421
Effective length of database: 425
Effective search space:   178925
Effective search space used:   178925
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 201398 SO2248 (L-serine dehydratase 1 (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.22135.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.1e-217  707.4   1.5   4.7e-217  707.2   1.5    1.0  1  lcl|FitnessBrowser__MR1:201398  SO2248 L-serine dehydratase 1 (N


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201398  SO2248 L-serine dehydratase 1 (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  707.2   1.5  4.7e-217  4.7e-217       1     450 []       2     455 ..       2     455 .. 0.99

  Alignments for each domain:
  == domain 1  score: 707.2 bits;  conditional E-value: 4.7e-217
                       TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpeevdi 79 
                                     isvfd+fkiGiGPssshtvGPmka+k f+++l + g++ q+++++ +l+Gsl+ tGkGh+t kav+lGl+Ge+pe+vd+
  lcl|FitnessBrowser__MR1:201398   2 ISVFDMFKIGIGPSSSHTVGPMKAGKIFMQHLADSGQIGQIDELRAELFGSLGQTGKGHGTGKAVILGLMGEDPETVDT 80 
                                     79***************************************************************************** PP

                       TIGR00720  80 esieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevlkektyysvGGGfivdeeelk 157
                                     +si+ +le+v ++++l+++  k +kf++e+ ++++ +++lp h+n+++l ay++  e + e+tyysvGGGfi+de+e++
  lcl|FitnessBrowser__MR1:201398  81 DSIDGILEHVSKSETLTISCGKVVKFTREDGITYHrRKSLPAHANAMTLYAYSKG-ECIFERTYYSVGGGFILDEDEIN 158
                                     ***********************************999**************987.9*********************9 PP

                       TIGR00720 158 keeeeee....evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeecierglkaegvlpGg 232
                                     +++++ +    ++py+f+s+a+llelC+e+glsis+++++ne +l+seeev+akl +iw++m++cierg ++eg+lpGg
  lcl|FitnessBrowser__MR1:201398 159 QRNASPAsqieSAPYDFNSSAQLLELCTEHGLSISSLMMANELSLASEEEVKAKLWNIWQTMKTCIERGYQKEGILPGG 237
                                     9988766667799****************************************************************** PP

                       TIGR00720 233 lkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekv 311
                                     lk++rra++l+r+lka+ +++ dpl+++dwv l+al+vne+naaG+rvvtaPtnGaagiiPavl yy++fv+e+  ++ 
  lcl|FitnessBrowser__MR1:201398 238 LKLRRRAPALYRRLKAEGRNNVDPLTAMDWVDLFALSVNEQNAAGDRVVTAPTNGAAGIIPAVLCYYDTFVQEVDIDVC 316
                                     ******************************************************************************* PP

                       TIGR00720 312 vrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiP 390
                                      r+llta+aiGilyk+nasisgaevGCqgevGvacsmaa++l+e++ggt+e venaaei+mehnlGltCdPvgGlvq+P
  lcl|FitnessBrowser__MR1:201398 317 ARYLLTAAAIGILYKKNASISGAEVGCQGEVGVACSMAAGALTEIMGGTVEHVENAAEIGMEHNLGLTCDPVGGLVQVP 395
                                     ******************************************************************************* PP

                       TIGR00720 391 CiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                     Cierna++a+kaina+r+al++dg++kvsldkvi+tm++tGkdm++kyket+kgGlav++
  lcl|FitnessBrowser__MR1:201398 396 CIERNAMGAIKAINASRMALRGDGNHKVSLDKVIKTMMDTGKDMRSKYKETAKGGLAVNI 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.28
//
[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