Alignments for a candidate for sdaB in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Shewanella amazonensis SB2B

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 6937155 Sama_1325 L-serine ammonia-lyase (RefSeq)

Query= BRENDA::P16095
         (454 letters)



>FitnessBrowser__SB2B:6937155
          Length = 458

 Score =  516 bits (1328), Expect = e-151
 Identities = 257/456 (56%), Positives = 333/456 (73%), Gaps = 6/456 (1%)

Query: 1   MISLFDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLLDSVTRVAVDVYGSLSLTGKGH 60
           MIS+FD+FK+GIGPSSSHTVGPMKAGK+FV  +   GLL  V  +  +++GSL  TGKGH
Sbjct: 1   MISVFDIFKIGIGPSSSHTVGPMKAGKEFVARVESMGLLAQVDELRAELFGSLGQTGKGH 60

Query: 61  HTDIAIIMGLAGNEPATVDIDSIPGFIRDVEERERLLLAQGRHEVDFPRDNGMRFHNGN- 119
            T  A+I+GL G +P TVD D+I G +  V  +E L LAQG+  V F R++G+ +H    
Sbjct: 61  GTGKAVILGLMGEDPETVDTDAIDGILAQVSSQETLTLAQGK-TVKFTREDGIIYHRRKT 119

Query: 120 LPLHENGMQIHAYNGDEVVYSKTYYSIGGGFIVDEEHFGQDAANEVS----VPYPFKSAT 175
           LP H N M ++A+ G E +Y +TYYS+GGGF++DE+   +   +  +     PY F SA 
Sbjct: 120 LPAHANAMTLYAFAGGECLYQRTYYSVGGGFVLDEDQIERKNPSPATPIKAAPYDFNSAQ 179

Query: 176 ELLAYCNETGYSLSGLAMQNELALHSKKEIDEYFAHVWQTMQACIDRGMNTEGVLPGPLR 235
           +LL  C + G S+S L MQNEL L S+ ++     H+WQTM+ CI++G   EG+LPG L+
Sbjct: 180 QLLEMCTDNGLSISSLMMQNELTLASEDDVKARLWHIWQTMKTCIEKGYKKEGMLPGGLK 239

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

Query: 296 VLAYYDHFIESVSPDIYTRYFMAAGAIGALYKMNASISGAEVGCQGEVGVACSMAAAGLA 355
           VL Y+D F++ V  DI  RY + A AIG LYK NASISGAEVGCQGEVGVACSMAAA L 
Sbjct: 300 VLCYFDTFVQQVDVDICARYLLTAAAIGILYKKNASISGAEVGCQGEVGVACSMAAAALT 359

Query: 356 ELLGGSPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINAARMALRRTS 415
           E++GG+ E V  AAEIGMEHNLGLTCDPV G VQVPCIERNA+ +VKAINA+R+ALR   
Sbjct: 360 EIMGGTVEHVENAAEIGMEHNLGLTCDPVGGLVQVPCIERNAMGAVKAINASRLALRGDG 419

Query: 416 APRVSLDKVIETMYETGKDMNAKYRETSRGGLAIKV 451
             +VSLDKVI+TM +TG+DM +KY+ET++GGLA+ +
Sbjct: 420 NHKVSLDKVIKTMMDTGRDMRSKYKETAKGGLAVNI 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: 628
Number of extensions: 24
Number of successful extensions: 2
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 6937155 Sama_1325 (L-serine ammonia-lyase (RefSeq))
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.19342.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-217  709.3   0.6   1.2e-217  709.1   0.6    1.0  1  lcl|FitnessBrowser__SB2B:6937155  Sama_1325 L-serine ammonia-lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937155  Sama_1325 L-serine ammonia-lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  709.1   0.6  1.2e-217  1.2e-217       1     450 []       2     455 ..       2     455 .. 0.99

  Alignments for each domain:
  == domain 1  score: 709.1 bits;  conditional E-value: 1.2e-217
                         TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpeev 77 
                                       isvfd+fkiGiGPssshtvGPmka+kefv++++++g l+qv++++ +l+Gsl+ tGkGh+t kav+lGl+Ge+pe+v
  lcl|FitnessBrowser__SB2B:6937155   2 ISVFDIFKIGIGPSSSHTVGPMKAGKEFVARVESMGLLAQVDELRAELFGSLGQTGKGHGTGKAVILGLMGEDPETV 78 
                                       79*************************************************************************** PP

                         TIGR00720  78 diesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevlkektyysvGGGfivde 153
                                       d++ i+ +l++v ++++l+la+ k++kf++e+ ++++ +++lp h+n+++l a+++  e l+++tyysvGGGf++de
  lcl|FitnessBrowser__SB2B:6937155  79 DTDAIDGILAQVSSQETLTLAQGKTVKFTREDGIIYHrRKTLPAHANAMTLYAFAGG-ECLYQRTYYSVGGGFVLDE 154
                                       *************************************999**************998.9****************** PP

                         TIGR00720 154 eelkkeeeeee....evpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeecierglkae 226
                                       +++++++ + +     +py+f+sa++lle+C+++glsis+++++ne +l+se++v+a+l +iw++m++cie+g k+e
  lcl|FitnessBrowser__SB2B:6937155 155 DQIERKNPSPAtpikAAPYDFNSAQQLLEMCTDNGLSISSLMMQNELTLASEDDVKARLWHIWQTMKTCIEKGYKKE 231
                                       ****9998877677789************************************************************ PP

                         TIGR00720 227 gvlpGglkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfv 303
                                       g+lpGglk++rra+ l+r+l+a+ +++ dpl+++dwv l+al+vne+naaG+rvvtaPtnGaagiiPavl y+++fv
  lcl|FitnessBrowser__SB2B:6937155 232 GMLPGGLKLRRRAPGLYRRLQAEGRNNVDPLNAMDWVDLFALSVNEQNAAGDRVVTAPTNGAAGIIPAVLCYFDTFV 308
                                       ***************************************************************************** PP

                         TIGR00720 304 eeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltC 380
                                       +++  ++  r+llta+aiGilyk+nasisgaevGCqgevGvacsmaaa+l+e++ggt+e venaaei+mehnlGltC
  lcl|FitnessBrowser__SB2B:6937155 309 QQVDVDICARYLLTAAAIGILYKKNASISGAEVGCQGEVGVACSMAAAALTEIMGGTVEHVENAAEIGMEHNLGLTC 385
                                       ***************************************************************************** PP

                         TIGR00720 381 dPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                       dPvgGlvq+PCierna++avkaina+rlal++dg++kvsldkvi+tm++tG+dm++kyket+kgGlav++
  lcl|FitnessBrowser__SB2B:6937155 386 DPVGGLVQVPCIERNAMGAVKAINASRLALRGDGNHKVSLDKVIKTMMDTGRDMRSKYKETAKGGLAVNI 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: 00:00:00.02
# Mc/sec: 9.29
//
[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