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 6938668 Sama_2771 L-serine ammonia-lyase (RefSeq)

Query= BRENDA::P16095
         (454 letters)



>FitnessBrowser__SB2B:6938668
          Length = 464

 Score =  580 bits (1494), Expect = e-170
 Identities = 300/456 (65%), Positives = 347/456 (76%), Gaps = 4/456 (0%)

Query: 1   MISLFDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLLDSVTRVAVDVYGSLSLTGKGH 60
           M S FD++K+GIGPSSSHTVGPMKA K FVD L    L   +  +  DVYGSLSLTGKGH
Sbjct: 11  MFSTFDIYKIGIGPSSSHTVGPMKAAKAFVDRLDTLNLSGRIDSLKADVYGSLSLTGKGH 70

Query: 61  HTDIAIIMGLAGNEPATVDIDSIPGFIRDVEERERLLLAQGRHEVDFPRDNGMRFHNGNL 120
           HTDIAI++GL G  P  VDID+I   I  V E E L L  GR  V F RD  M FH   L
Sbjct: 71  HTDIAIVLGLMGQSPECVDIDAIGATIAAVNESETLWLESGR-PVRFARD-AMVFHPHAL 128

Query: 121 PLHENGMQIHAYNGDEVVYSKTYYSIGGGFIVDEEHFGQDAANEVSVPYPFKSATELLAY 180
           PLHEN M + A+ GDE++ S TYYSIGGGF+V+E  FG+    E   PYPF+ A  L+  
Sbjct: 129 PLHENAMTLSAFAGDELLASNTYYSIGGGFVVEEADFGKAQIGETLFPYPFEDAERLVQL 188

Query: 181 CNETGYSLSGLAMQNELALHSKKEIDEYFAHVWQTMQACIDRGMNTEGVLPGPLRVPRRA 240
           C   G S+S L + NE   HS++ I   F  +W TM+  IDRG +TEGVL GPLRVPRRA
Sbjct: 189 CRAEGVSISTLMLANEKDCHSEEYIYRGFRDIWLTMKQAIDRGCHTEGVLAGPLRVPRRA 248

Query: 241 SALRRMLVSSDKLSNDPMNVIDWVNMFALAVNEENAAGGRVVTAPTNGACGIVPAVLAYY 300
            AL + L +S ++S DPM ++DWVN+FALAV+EENAAGGRVVTAPTNGA GI+PAV+AY+
Sbjct: 249 PALLKQLETSGRISADPMEIVDWVNLFALAVSEENAAGGRVVTAPTNGAAGIIPAVMAYF 308

Query: 301 DHFIESVSPDIYTRYFMAAGAIGALYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGG 360
           D FI+ +    Y+R+ +A+ AIG+LYK NASISGAEVGCQGEVGVACSMAAAGLAEL+G 
Sbjct: 309 DRFIQPLGQKEYSRFLLASAAIGSLYKRNASISGAEVGCQGEVGVACSMAAAGLAELMGA 368

Query: 361 SPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINAARMALRRTSAPRVS 420
           SP QVC+AAEI MEHNLGLTCDPVAGQVQVPCIERNAIA+VKA+NAARMALRRTS PRVS
Sbjct: 369 SPAQVCMAAEIAMEHNLGLTCDPVAGQVQVPCIERNAIAAVKAVNAARMALRRTSDPRVS 428

Query: 421 LDKVIETMYETGKDMNAKYRETSRGGLAIKVQ--CD 454
           LDKVI TMYETGKDM+AKYRETS GGLAIKV   CD
Sbjct: 429 LDKVIATMYETGKDMHAKYRETSLGGLAIKVTSICD 464


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: 616
Number of extensions: 26
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: 464
Length adjustment: 33
Effective length of query: 421
Effective length of database: 431
Effective search space:   181451
Effective search space used:   181451
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 6938668 Sama_2771 (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.15125.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.2e-211  687.9   0.1   3.7e-211  687.7   0.1    1.0  1  lcl|FitnessBrowser__SB2B:6938668  Sama_2771 L-serine ammonia-lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6938668  Sama_2771 L-serine ammonia-lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  687.7   0.1  3.7e-211  3.7e-211       2     450 .]      13     459 ..      12     459 .. 0.99

  Alignments for each domain:
  == domain 1  score: 687.7 bits;  conditional E-value: 3.7e-211
                         TIGR00720   2 svfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpeevd 78 
                                       s+fd++kiGiGPssshtvGPmkaak+fv++l++ +   +++++k d+yGsl+ltGkGh+td a++lGl+G++pe vd
  lcl|FitnessBrowser__SB2B:6938668  13 STFDIYKIGIGPSSSHTVGPMKAAKAFVDRLDTLNLSGRIDSLKADVYGSLSLTGKGHHTDIAIVLGLMGQSPECVD 89 
                                       99*************************************************************************** PP

                         TIGR00720  79 iesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGGGfivdeee 155
                                       i+ i + +++v+e+++l l++   ++f  ++ ++f+ ++lplhen+++l+a++++ e+l+++tyys+GGGf+v+e++
  lcl|FitnessBrowser__SB2B:6938668  90 IDAIGATIAAVNESETLWLESGRPVRFA-RDAMVFHPHALPLHENAMTLSAFAGD-ELLASNTYYSIGGGFVVEEAD 164
                                       ***************************9.6789*********************9.9******************** PP

                         TIGR00720 156 lkkeeeeeeevpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeecierglkaegvlpGg 232
                                       ++k +  e+  pypf+ a+ l++lC++eg+sis+++l+nek ++see + + + +iw +m+++i+rg+++egvl+G+
  lcl|FitnessBrowser__SB2B:6938668 165 FGKAQIGETLFPYPFEDAERLVQLCRAEGVSISTLMLANEKDCHSEEYIYRGFRDIWLTMKQAIDRGCHTEGVLAGP 241
                                       ***************************************************************************** PP

                         TIGR00720 233 lkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeasee 309
                                       l+v+rra++l ++l+++ + s+dp++++dwvnl+alav+eenaaGgrvvtaPtnGaagiiPav+ay+++f++   ++
  lcl|FitnessBrowser__SB2B:6938668 242 LRVPRRAPALLKQLETSGRISADPMEIVDWVNLFALAVSEENAAGGRVVTAPTNGAAGIIPAVMAYFDRFIQPLGQK 318
                                       ***************************************************************************** PP

                         TIGR00720 310 kvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGl 386
                                       ++ rfll+++aiG+lyk+nasisgaevGCqgevGvacsmaaaglael+g++p qv++aaeiamehnlGltCdPv+G+
  lcl|FitnessBrowser__SB2B:6938668 319 EYSRFLLASAAIGSLYKRNASISGAEVGCQGEVGVACSMAAAGLAELMGASPAQVCMAAEIAMEHNLGLTCDPVAGQ 395
                                       ***************************************************************************** PP

                         TIGR00720 387 vqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                       vq+PCiernaiaavka+naar+al+++++++vsldkvi+tm+etGkdm+aky+ets gGla+kv
  lcl|FitnessBrowser__SB2B:6938668 396 VQVPCIERNAIAAVKAVNAARMALRRTSDPRVSLDKVIATMYETGKDMHAKYRETSLGGLAIKV 459
                                       **************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (464 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.49
//
[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