Alignments for a candidate for sdaB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Klebsiella michiganensis M5al

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate BWI76_RS14470 BWI76_RS14470 L-serine ammonia-lyase

Query= BRENDA::P30744
         (455 letters)



>FitnessBrowser__Koxy:BWI76_RS14470
          Length = 455

 Score =  658 bits (1697), Expect = 0.0
 Identities = 321/455 (70%), Positives = 377/455 (82%), Gaps = 1/455 (0%)

Query: 1   MISVFDIFKIGIGPSSSHTVGPMKAGKQFTDDLIARNLLKDVTRVVVDVYGSLSLTGKGH 60
           MISVFDIFKI IGPSSSHTVGPMKAGK F D L  + LL  VTR+VVDVYGSLSLTGKGH
Sbjct: 1   MISVFDIFKISIGPSSSHTVGPMKAGKHFVDTLQEKGLLHKVTRLVVDVYGSLSLTGKGH 60

Query: 61  HTDIAIIMGLAGNLPDTVDIDSIPSFIQDVNTHGRLMLANGQHEVEFPVDQCMNFHADNL 120
           HTDIAII+GL+G LPDTVDID+IP  I+DVN   RL +  GQ E+EFPV +CM FH + L
Sbjct: 61  HTDIAIILGLSGYLPDTVDIDAIPDIIRDVNVMHRLFIEEGQREIEFPVAECMRFHNEFL 120

Query: 121 SLHENGMRITALAGDKVVYSQTYYSIGGGFIVDEEHFGQQDSAPVEVPYPYSSAADLQKH 180
            LHENGM ITA    K+ + QTYYSIGGGFIV EE+FG+   A V++P+P+ SA +L  H
Sbjct: 121 PLHENGMSITAFCDGKIAHFQTYYSIGGGFIVTEENFGKSQGAEVDIPFPFYSARNLLAH 180

Query: 181 CQETGLSLSGLMMKNELALHSKEELEQHLANVWEVMRGGIERGISTEGVLPGKLRVPRRA 240
           CQ+  LS+S +MMKNE+A H +E +EQ++A +WE MR  I RG++TEG+LPG L+VPRRA
Sbjct: 181 CQDNCLSISAVMMKNEIARHGRESVEQNMAKIWETMRNAINRGMNTEGILPGPLKVPRRA 240

Query: 241 AALRRMLVSQDKTTTDPMAVVDWINMFALAVNEENAAGGRVVTAPTNGACGIIPAVLAYY 300
           +AL R+L  Q ++ T P++ +DW+NMFA+AV EENAAGGRVVTAPTNGACGI+PAVLAYY
Sbjct: 241 SALHRVLAPQSQSIT-PLSAMDWVNMFAMAVGEENAAGGRVVTAPTNGACGIVPAVLAYY 299

Query: 301 DKFIREVNANSLARYLLVASAIGSLYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGA 360
           D+FI+EV      RY L A AIG LYKMNASISGAEVGCQGEVGVACSMA+AGLAELLG 
Sbjct: 300 DRFIKEVTPEISMRYFLTAGAIGILYKMNASISGAEVGCQGEVGVACSMASAGLAELLGG 359

Query: 361 SPAQVCIAAEIAMEHNLGLTCDPVAGQVQVPCIERNAIAAVKAVNAARMALRRTSEPRVC 420
           SP +VCIAAEI MEHNLGLTCDPVAGQVQVPCIERNAIAAVKA+N+A MA+ RTS+P+V 
Sbjct: 360 SPEKVCIAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIAAVKAINSASMAMYRTSDPKVS 419

Query: 421 LDKVIETMYETGKDMNAKYRETSRGGLAMKIVACD 455
           LDKVIETM+ETGKDMNAKYRET+RGGLA+K+  C+
Sbjct: 420 LDKVIETMFETGKDMNAKYRETARGGLAIKVAVCE 454


Lambda     K      H
   0.319    0.134    0.388 

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: 613
Number of extensions: 19
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: 455
Length of database: 455
Length adjustment: 33
Effective length of query: 422
Effective length of database: 422
Effective search space:   178084
Effective search space used:   178084
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 BWI76_RS14470 BWI76_RS14470 (L-serine ammonia-lyase)
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.6008.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   7.3e-218  709.8   0.5   8.3e-218  709.7   0.5    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS14470  BWI76_RS14470 L-serine ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS14470  BWI76_RS14470 L-serine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  709.7   0.5  8.3e-218  8.3e-218       1     450 []       2     450 ..       2     450 .. 0.99

  Alignments for each domain:
  == domain 1  score: 709.7 bits;  conditional E-value: 8.3e-218
                               TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleG 71 
                                             isvfd+fki iGPssshtvGPmka+k+fv++l++kg l++v+r+ vd+yGsl+ltGkGh+td a++lGl G
  lcl|FitnessBrowser__Koxy:BWI76_RS14470   2 ISVFDIFKISIGPSSSHTVGPMKAGKHFVDTLQEKGLLHKVTRLVVDVYGSLSLTGKGHHTDIAIILGLSG 72 
                                             79********************************************************************* PP

                               TIGR00720  72 elpeevdiesieklleeveeekklkla.nqkeikfdlekdlafkdevlplhenglrlkaydeegevlkekt 141
                                             +lp++vdi+ i++++++v+  ++l ++ +q ei+f +++ ++f++e+lplheng++++a+ +  ++ + +t
  lcl|FitnessBrowser__Koxy:BWI76_RS14470  73 YLPDTVDIDAIPDIIRDVNVMHRLFIEeGQREIEFPVAECMRFHNEFLPLHENGMSITAFCDG-KIAHFQT 142
                                             **************************98899*****************************987.89999** PP

                               TIGR00720 142 yysvGGGfivdeeelkkeeeeeeevpypfksaaellelCkeeglsisevvlenekalrseeevraklleiw 212
                                             yys+GGGfiv+ee+++k++  e+++p+pf sa++ll++C+++ lsis+v+++ne a ++ e+v++++++iw
  lcl|FitnessBrowser__Koxy:BWI76_RS14470 143 YYSIGGGFIVTEENFGKSQGAEVDIPFPFYSARNLLAHCQDNCLSISAVMMKNEIARHGRESVEQNMAKIW 213
                                             *********************************************************************** PP

                               TIGR00720 213 kvmeecierglkaegvlpGglkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvta 283
                                             ++m+++i+rg+++eg+lpG+lkv+rra++l+r l  ++++  +pl+++dwvn++a+av eenaaGgrvvta
  lcl|FitnessBrowser__Koxy:BWI76_RS14470 214 ETMRNAINRGMNTEGILPGPLKVPRRASALHRVLAPQSQS-ITPLSAMDWVNMFAMAVGEENAAGGRVVTA 283
                                             ********************************99988877.69**************************** PP

                               TIGR00720 284 PtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaagla 354
                                             PtnGa+gi+Pavlayy++f++e++ e+ +r++ltagaiGilyk+nasisgaevGCqgevGvacsma+agla
  lcl|FitnessBrowser__Koxy:BWI76_RS14470 284 PTNGACGIVPAVLAYYDRFIKEVTPEISMRYFLTAGAIGILYKMNASISGAEVGCQGEVGVACSMASAGLA 354
                                             *********************************************************************** PP

                               TIGR00720 355 ellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvie 425
                                             ellgg+pe+v++aaei+mehnlGltCdPv+G+vq+PCiernaiaavkain+a +a+ +++++kvsldkvie
  lcl|FitnessBrowser__Koxy:BWI76_RS14470 355 ELLGGSPEKVCIAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIAAVKAINSASMAMYRTSDPKVSLDKVIE 425
                                             *********************************************************************** PP

                               TIGR00720 426 tmretGkdmkakyketskgGlavkv 450
                                             tm etGkdm+aky+et++gGla+kv
  lcl|FitnessBrowser__Koxy:BWI76_RS14470 426 TMFETGKDMNAKYRETARGGLAIKV 450
                                             ***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (455 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: 10.05
//
[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