Alignments for a candidate for sdaB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Phaeobacter inhibens BS107

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate GFF2346 PGA1_c23770 L-serine dehydratase TdcG

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4954
         (458 letters)



>FitnessBrowser__Phaeo:GFF2346
          Length = 457

 Score =  438 bits (1126), Expect = e-127
 Identities = 236/460 (51%), Positives = 305/460 (66%), Gaps = 5/460 (1%)

Query: 1   MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALVDHGFLADVRRVEIRLYGSLSATGVG 60
           M +SVFD+FKVGIGPSSSHT+GPM AAA F   +    F  +   +   L+GSL+ TGVG
Sbjct: 1   MFLSVFDMFKVGIGPSSSHTMGPMVAAAKFLDLMRASPF--EFHGLRASLHGSLAFTGVG 58

Query: 61  HATDRACVMGLMGEWPDRIDPTTIDSRIHTLRETGKLCLAGVAQIAFDWQRDLLL-LDES 119
           HATDRA ++GL G      D     + +  L +T  +   G+  + FD + D++   D +
Sbjct: 59  HATDRATILGLGGFVAHDYDDEKAVAFLAELDKTHTMHPEGLGALHFDPKADMIFDYDHA 118

Query: 120 LPYHPNAMSLTAFGETGE-LFEQTYYSVGGGFIIEAAEAESGIAPAGDVVLPYDFSSAAE 178
           LP H N M L A    G+ +  Q YYS+GGGF++   E  +G A      +PY F SAAE
Sbjct: 119 LPGHANGMILMATDAQGDVILRQVYYSIGGGFVLTEEELAAGKATDEGEPVPYPFKSAAE 178

Query: 179 LLKLCNEHGLRVGELMMANERAWRSDAEIRQGLLHIWSVMRECVEQGLRHEGILPGGLSV 238
           +L++    G  +  +  ANE A   +  + +G   IW VM +C+ +GL  +GILPGGL+V
Sbjct: 179 MLEMAKASGKSIAGMKRANEIARGCEVSLAKGTARIWQVMNDCINRGLERDGILPGGLNV 238

Query: 239 PRRAAKLHRSLQEIGKPNVITSTLSAMEWVNLYALAVNEENAAGGRMVTAPTNGAAGIIP 298
            RRA  +H +LQ     N I +  +  +W+++YA+AVNEENAAGG++VTAPTNGAAG +P
Sbjct: 239 RRRAKGIHDALQAERGMN-INAPHTINDWMSVYAMAVNEENAAGGQVVTAPTNGAAGTLP 297

Query: 299 AVLHYYMKFNADASDDDVVAFFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGL 358
           AV+ YY+     A++  V  F L AAA+  L K NASISGAE GCQ EVGSA AM+AAGL
Sbjct: 298 AVIRYYLDHVPGAAETHVEDFLLTAAAIAGLVKYNASISGAEAGCQAEVGSAAAMSAAGL 357

Query: 359 AEVLGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGD 418
             V+G TPEQ+ENAAEI LEH+LG+TCDPV GLVQVPCIERN +AA+KA++A  +ALRGD
Sbjct: 358 CAVMGGTPEQVENAAEIALEHHLGMTCDPVKGLVQVPCIERNGLAAIKAVSAASLALRGD 417

Query: 419 GKHFISLDRVIRTMRDTGADMHDKYKETSRGGLAVNWVEC 458
           G+HF+ LD  I TMR TG DMHDKYKETS GGLAVN   C
Sbjct: 418 GQHFVPLDACIETMRQTGEDMHDKYKETSLGGLAVNVPNC 457


Lambda     K      H
   0.320    0.135    0.404 

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: 553
Number of extensions: 23
Number of successful extensions: 5
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: 457
Length adjustment: 33
Effective length of query: 425
Effective length of database: 424
Effective search space:   180200
Effective search space used:   180200
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 GFF2346 PGA1_c23770 (L-serine dehydratase TdcG)
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.24824.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.3e-182  591.9   2.4   4.9e-182  591.7   2.4    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2346  PGA1_c23770 L-serine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2346  PGA1_c23770 L-serine dehydratase TdcG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  591.7   2.4  4.9e-182  4.9e-182       2     450 .]       4     454 ..       3     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: 591.7 bits;  conditional E-value: 4.9e-182
                          TIGR00720   2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpeev 77 
                                        svfd+fk+GiGPsssht+GPm aa++f++ ++      + + ++  l+Gsla+tG Gh+td+a +lGl G+ +++ 
  lcl|FitnessBrowser__Phaeo:GFF2346   4 SVFDMFKVGIGPSSSHTMGPMVAAAKFLDLMRAS--PFEFHGLRASLHGSLAFTGVGHATDRATILGLGGFVAHDY 77 
                                        9***************************998655..556899********************************** PP

                          TIGR00720  78 diesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevlkektyysvGGGfivd 152
                                        d e++ ++l+e+ ++++++ ++   ++fd + d++f+ d++lp h+ng+ l a d +g+v+ +++yys+GGGf+++
  lcl|FitnessBrowser__Phaeo:GFF2346  78 DDEKAVAFLAELDKTHTMHPEGLGALHFDPKADMIFDyDHALPGHANGMILMATDAQGDVILRQVYYSIGGGFVLT 153
                                        *************************************9************************************** PP

                          TIGR00720 153 eeelkkeeeeee..evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeecierglkae 226
                                        eeel   ++++e   vpypfksaae+le+ k++g+si+ +  +ne a   e +  +  ++iw+vm++ci+rgl+++
  lcl|FitnessBrowser__Phaeo:GFF2346 154 EEELAAGKATDEgePVPYPFKSAAEMLEMAKASGKSIAGMKRANEIARGCEVSLAKGTARIWQVMNDCINRGLERD 229
                                        **9887766666569************************************************************* PP

                          TIGR00720 227 gvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykk 301
                                        g+lpGgl+v+rra+ +++ l+a++ ++ ++p ++ dw+++ya+avneenaaGg+vvtaPtnGaag +Pav++yy  
  lcl|FitnessBrowser__Phaeo:GFF2346 230 GILPGGLNVRRRAKGIHDALQAERGMNiNAPHTINDWMSVYAMAVNEENAAGGQVVTAPTNGAAGTLPAVIRYYLD 305
                                        ************************99989999******************************************** PP

                          TIGR00720 302 fveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlG 377
                                         v+ a+e +v++fllta+ai  l k nasisgae+GCq+evG+a++m+aagl++++ggtpeqvenaaeia+eh+lG
  lcl|FitnessBrowser__Phaeo:GFF2346 306 HVPGAAETHVEDFLLTAAAIAGLVKYNASISGAEAGCQAEVGSAAAMSAAGLCAVMGGTPEQVENAAEIALEHHLG 381
                                        **************************************************************************** PP

                          TIGR00720 378 ltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                        +tCdPv Glvq+PCiern++aa+ka++aa lal++dg+++v ld  ietmr+tG+dm+ kykets gGlav+v
  lcl|FitnessBrowser__Phaeo:GFF2346 382 MTCDPVKGLVQVPCIERNGLAAIKAVSAASLALRGDGQHFVPLDACIETMRQTGEDMHDKYKETSLGGLAVNV 454
                                        ***********************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (457 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: 12.09
//
[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