Alignments for a candidate for sdaB in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Sinorhizobium meliloti 1021

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate SMc01256 SMc01256 L-serine dehydratase

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



>FitnessBrowser__Smeli:SMc01256
          Length = 466

 Score =  475 bits (1223), Expect = e-138
 Identities = 248/468 (52%), Positives = 328/468 (70%), Gaps = 12/468 (2%)

Query: 1   MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALVDHGFL----ADVRRVEIRLYGSLSA 56
           M +SVFD+FK+GIGPSSSHT+GPM AA  F   ++   +     A V  +++ L+GSL+ 
Sbjct: 1   MFLSVFDVFKIGIGPSSSHTMGPMSAANRFLDLILSDEWPRPSHAAVGAIKVSLHGSLAH 60

Query: 57  TGVGHATDRACVMGLMGEWPDRIDPTTIDSRIHTLRETGKLCLAGVAQIAFDWQRDLLLL 116
           TG+GH T RA ++GLMGE PD ++P  +D  I  +  TG++   G A   F  + DL+  
Sbjct: 61  TGIGHGTGRAVILGLMGERPDLVEPDGMDGIIEQVERTGRITPPGHAGYMFQPKTDLVFD 120

Query: 117 DES-LPYHPNAMSLTAFGETGELF-EQTYYSVGGGFIIEAAEAESGIA----PAGDVVLP 170
            ++ LP H N MS +AF   G L  ++ YYS+GGGF++   E ++  A    PAG V +P
Sbjct: 121 KKTPLPGHANGMSFSAFDRDGRLLLKRIYYSIGGGFVVTDTELDAMRAQKNKPAG-VKVP 179

Query: 171 YDFSSAAELLKLCNEHGLRVGELMMANERAWRSDAEIRQGLLHIWSVMRECVEQGLRHEG 230
           Y F++A ++L +    GL + ++  ANE    S  E+  GL  IW+ M  C+++GL  +G
Sbjct: 180 YPFATAQQMLDMAARSGLTIAQMKRANEECRMSRDELDAGLDRIWTAMSSCIDRGLSQDG 239

Query: 231 ILPGGLSVPRRAAKLHRSLQEIGKPNVITSTLSAMEWVNLYALAVNEENAAGGRMVTAPT 290
           I+PGGL V RRA  +H  LQE  + N  T+ L A +W+++YA+AVNEENAAGGR+VT+PT
Sbjct: 240 IMPGGLKVRRRARAIHDKLQEEWRSNK-TNPLLANDWLSVYAMAVNEENAAGGRVVTSPT 298

Query: 291 NGAAGIIPAVLHYYMKFNADASDDDVVAFFLGAAAVGILCKKNASISGAEVGCQGEVGSA 350
           NGAAG++PA + YY+ F+ DA  + +  + L AAA+G + K NASISGAEVGCQGEVGSA
Sbjct: 299 NGAAGVVPATIRYYLHFHDDADQEGIRDYLLTAAAIGGIIKHNASISGAEVGCQGEVGSA 358

Query: 351 CAMAAAGLAEVLGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINA 410
            AMAAAGLA V+G TPEQ+ENAAEI LEH+LG+TCDPV GLVQVPCIERNA+ AVKA+ A
Sbjct: 359 SAMAAAGLAAVMGGTPEQIENAAEIALEHHLGMTCDPVAGLVQVPCIERNALGAVKAVTA 418

Query: 411 TQMALRGDGKHFISLDRVIRTMRDTGADMHDKYKETSRGGLAVNWVEC 458
             +AL+GDGKHF+ LD  I TMR TGADM++KYKETS GGLAVN VEC
Sbjct: 419 ASLALKGDGKHFVPLDACIETMRQTGADMNEKYKETSTGGLAVNVVEC 466


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: 571
Number of extensions: 16
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: 466
Length adjustment: 33
Effective length of query: 425
Effective length of database: 433
Effective search space:   184025
Effective search space used:   184025
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 SMc01256 SMc01256 (L-serine dehydratase)
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.24972.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.5e-191  622.4   0.0   2.9e-191  622.2   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc01256  SMc01256 L-serine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01256  SMc01256 L-serine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  622.2   0.0  2.9e-191  2.9e-191       2     450 .]       4     463 ..       3     463 .. 0.96

  Alignments for each domain:
  == domain 1  score: 622.2 bits;  conditional E-value: 2.9e-191
                           TIGR00720   2 svfdlfkiGiGPssshtvGPmkaakefveelkk....kgkleqvkrvkvdlyGslaltGkGhktdkavllGleGe 72 
                                         svfd+fkiGiGPsssht+GPm aa++f++ + +    + + ++v ++kv l+Gsla tG Gh+t +av+lGl+Ge
  lcl|FitnessBrowser__Smeli:SMc01256   4 SVFDVFKIGIGPSSSHTMGPMSAANRFLDLILSdewpRPSHAAVGAIKVSLHGSLAHTGIGHGTGRAVILGLMGE 78 
                                         9***************************98766122244678999****************************** PP

                           TIGR00720  73 lpeevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevlkektyysvG 146
                                          p+ v+ + ++ ++e+ve++++++  ++    f+ ++dl+f+ ++ lp h+ng++++a+d++g++l ++ yys+G
  lcl|FitnessBrowser__Smeli:SMc01256  79 RPDLVEPDGMDGIIEQVERTGRITPPGHAGYMFQPKTDLVFDkKTPLPGHANGMSFSAFDRDGRLLLKRIYYSIG 153
                                         *****************************************98899***************************** PP

                           TIGR00720 147 GGfivdeeelkkeeeeee.....evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvme 216
                                         GGf+v+++el+  +++++     +vpypf +a+++l++ +++gl+i+++  +ne++  s +e +a l +iw++m+
  lcl|FitnessBrowser__Smeli:SMc01256 154 GGFVVTDTELDAMRAQKNkpagvKVPYPFATAQQMLDMAARSGLTIAQMKRANEECRMSRDELDAGLDRIWTAMS 228
                                         *******99887665555567889*************************************************** PP

                           TIGR00720 217 ecierglkaegvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavneenaaGgrvvtaPtnGaag 290
                                         +ci+rgl+++g++pGglkv+rra ++++kl+++ +++ ++pl + dw+++ya+avneenaaGgrvvt+PtnGaag
  lcl|FitnessBrowser__Smeli:SMc01256 229 SCIDRGLSQDGIMPGGLKVRRRARAIHDKLQEEWRSNkTNPLLANDWLSVYAMAVNEENAAGGRVVTSPTNGAAG 303
                                         ********************************99888678999******************************** PP

                           TIGR00720 291 iiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqve 365
                                         ++Pa ++yy +f ++a +e + ++llta+aiG + k+nasisgaevGCqgevG+a++maaagla+++ggtpeq+e
  lcl|FitnessBrowser__Smeli:SMc01256 304 VVPATIRYYLHFHDDADQEGIRDYLLTAAAIGGIIKHNASISGAEVGCQGEVGSASAMAAAGLAAVMGGTPEQIE 378
                                         *************************************************************************** PP

                           TIGR00720 366 naaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyke 440
                                         naaeia+eh+lG+tCdPv+Glvq+PCierna++avka+ aa lalk+dgk++v ld  ietmr+tG+dm++kyke
  lcl|FitnessBrowser__Smeli:SMc01256 379 NAAEIALEHHLGMTCDPVAGLVQVPCIERNALGAVKAVTAASLALKGDGKHFVPLDACIETMRQTGADMNEKYKE 453
                                         *************************************************************************** PP

                           TIGR00720 441 tskgGlavkv 450
                                         ts gGlav+v
  lcl|FitnessBrowser__Smeli:SMc01256 454 TSTGGLAVNV 463
                                         ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (466 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: 7.58
//
[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