Alignments for a candidate for sdaB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Dinoroseobacter shibae DFL-12

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 3608720 Dshi_5008 L-serine dehydratase (NCBI)

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



>FitnessBrowser__Dino:3608720
          Length = 470

 Score =  442 bits (1138), Expect = e-129
 Identities = 239/471 (50%), Positives = 311/471 (66%), Gaps = 6/471 (1%)

Query: 1   MSVSVFDLFKIGIGPSSSHTVGPMIAARQFACHVQGTL----GLDAVHHVTVELFGSLSA 56
           M +SVFD+FK+G+GPSSSHT+GPM AA +F   ++G      G   +  +   L GSL+ 
Sbjct: 1   MFLSVFDIFKVGVGPSSSHTMGPMTAAARFLDDLRGGAERIPGAGKLARLGASLHGSLAF 60

Query: 57  TGVGHGTDKAVLLGLAGHEPDHIDPDQILPAIADIRTRQTLALLGEHPVPFVEKEHLLFR 116
           TG GH TD+AV+LGL G+ PD +DPD      A++R  + ++  G   + F  +  L+F 
Sbjct: 61  TGKGHATDRAVILGLIGYLPDTLDPDAAEKLEAEVRGTKRISPPGLGTLAFDPETDLVFD 120

Query: 117 R-KSLPLHPNGMAFHAFDAQGNEIATREYYSVGGGFVIDAAGERVLNSAATAGPDAVGHA 175
               LP H NG+  +A+D QGN   T+ YYSVGGGFV+  A      SAA+        A
Sbjct: 121 YGPPLPGHANGLVLNAYDEQGNLYMTQTYYSVGGGFVVTEAELEREKSAASNDLHDEKAA 180

Query: 176 QGLPHPFRTGAELLAQCQATGLTPAQLMAANEQHWRSASEVRRQLMAIWKTMAGAVQRGC 235
            G P+PF + AE+LA  QA+GL+ AQ+  ANE+   S   + +++ A+   M   + RG 
Sbjct: 181 MGYPYPFGSAAEMLAMGQASGLSIAQMKRANEEA-HSGPGLNKRIDAVCAVMDACIDRGL 239

Query: 236 ASTGTLPGPMHVRRRAAELHHKLSSAPEAALRDPLSMLDWVNLYAMAVNEENAAGGRVVT 295
              G LPG + V+RRA  +H +L +        P    DW+++YAMAVNEENAAGGRVVT
Sbjct: 240 RMDGILPGGLKVKRRAKAIHEQLLAERGQNQSQPHVANDWLSVYAMAVNEENAAGGRVVT 299

Query: 296 APTNGAAGVIPAVLHYYVNFLPGANEDGIATFLLTAGAIGIIYKENASLSGAEVGCQGEV 355
           +PTNGAAGV+PAV+ YY +   GA  +G+ TF+LTA AIG + K NAS+SGAE+GCQGEV
Sbjct: 300 SPTNGAAGVVPAVIRYYRDHCIGATAEGVRTFMLTASAIGGLIKHNASISGAEMGCQGEV 359

Query: 356 GVACSMAAGALAAVMGGSPEQIENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAIKA 415
           G A +MAA    A MGG+  QIENAAEI +EH+LGMTCDP  GLVQ+PCIERN +GAIKA
Sbjct: 360 GSASAMAAAGFCAAMGGTNAQIENAAEIALEHHLGMTCDPAAGLVQVPCIERNGLGAIKA 419

Query: 416 INAARMALRGDGQHVVSLDKVIKTMMQTGADMKVKYKETSRGGLAVNVVEC 466
           ++AA +ALRGDG H + LD  I+TM QTG DM  KYKETS GGLAVN+ EC
Sbjct: 420 VSAASLALRGDGTHFMPLDNCIETMRQTGHDMLTKYKETSLGGLAVNLPEC 470


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: 672
Number of extensions: 34
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: 466
Length of database: 470
Length adjustment: 33
Effective length of query: 433
Effective length of database: 437
Effective search space:   189221
Effective search space used:   189221
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 3608720 Dshi_5008 (L-serine dehydratase (NCBI))
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.2701.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-180  586.9   0.5   1.6e-180  586.7   0.5    1.0  1  lcl|FitnessBrowser__Dino:3608720  Dshi_5008 L-serine dehydratase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608720  Dshi_5008 L-serine dehydratase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  586.7   0.5  1.6e-180  1.6e-180       2     450 .]       4     467 ..       3     467 .. 0.95

  Alignments for each domain:
  == domain 1  score: 586.7 bits;  conditional E-value: 1.6e-180
                         TIGR00720   2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgk....leqvkrvkvdlyGslaltGkGhktdkavllGleGelp 74 
                                       svfd+fk+G+GPsssht+GPm aa++f+++l+  ++      +++r+   l+Gsla+tGkGh+td+av+lGl G+lp
  lcl|FitnessBrowser__Dino:3608720   4 SVFDIFKVGVGPSSSHTMGPMTAAARFLDDLRGGAEripgAGKLARLGASLHGSLAFTGKGHATDRAVILGLIGYLP 80 
                                       9******************************864332222468999******************************* PP

                         TIGR00720  75 eevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevlkektyysvGGGfi 150
                                       +++d + +ekl +ev+ +k+++  +  ++ fd e+dl+f+    lp h+ngl l+ayde+g++ +++tyysvGGGf+
  lcl|FitnessBrowser__Dino:3608720  81 DTLDPDAAEKLEAEVRGTKRISPPGLGTLAFDPETDLVFDyGPPLPGHANGLVLNAYDEQGNLYMTQTYYSVGGGFV 157
                                       ****************************************8899********************************* PP

                         TIGR00720 151 vdeeelkkeeeeee..........evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmee 217
                                       v+e+el++e++ ++            pypf saae+l++ +++glsi+++  +ne+a       ++++ ++  vm +
  lcl|FitnessBrowser__Dino:3608720 158 VTEAELEREKSAASndlhdekaamGYPYPFGSAAEMLAMGQASGLSIAQMKRANEEAHS-GPGLNKRIDAVCAVMDA 233
                                       ***999887665444455555656689****************************9977.678999*********** PP

                         TIGR00720 218 cierglkaegvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiP 293
                                       ci+rgl+ +g+lpGglkvkrra++++++l a++ ++ ++p  + dw+++ya+avneenaaGgrvvt+PtnGaag++P
  lcl|FitnessBrowser__Dino:3608720 234 CIDRGLRMDGILPGGLKVKRRAKAIHEQLLAERGQNqSQPHVANDWLSVYAMAVNEENAAGGRVVTSPTNGAAGVVP 310
                                       ****************************9999888747788899********************************* PP

                         TIGR00720 294 avlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaei 370
                                       av++yy+  +  a+ e v  f+lta+aiG l k+nasisgae+GCqgevG+a++maaag+++++ggt  q+enaaei
  lcl|FitnessBrowser__Dino:3608720 311 AVIRYYRDHCIGATAEGVRTFMLTASAIGGLIKHNASISGAEMGCQGEVGSASAMAAAGFCAAMGGTNAQIENAAEI 387
                                       ***************************************************************************** PP

                         TIGR00720 371 amehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGla 447
                                       a+eh+lG+tCdP +Glvq+PCiern+++a+ka++aa lal++dg++++ ld+ ietmr+tG+dm +kykets gGla
  lcl|FitnessBrowser__Dino:3608720 388 ALEHHLGMTCDPAAGLVQVPCIERNGLGAIKAVSAASLALRGDGTHFMPLDNCIETMRQTGHDMLTKYKETSLGGLA 464
                                       ***************************************************************************** PP

                         TIGR00720 448 vkv 450
                                       v++
  lcl|FitnessBrowser__Dino:3608720 465 VNL 467
                                       985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (470 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.24
//
[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