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.11429.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.69
//
[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:

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:

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:

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:

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