GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argG in Pedobacter sp. GW460-11-11-14-LB5

Align arginosuccinate synthetase (EC 6.3.4.5) (characterized)
to candidate CA265_RS18545 CA265_RS18545 argininosuccinate synthase

Query= reanno::Btheta:353286
         (402 letters)



>FitnessBrowser__Pedo557:CA265_RS18545
          Length = 395

 Score =  442 bits (1137), Expect = e-129
 Identities = 214/389 (55%), Positives = 285/389 (73%), Gaps = 1/389 (0%)

Query: 6   KKVVVAFSGGLDTSFTVMYLAKEKGYEVYAACANTGGFSEEQLKTNEENAYKLGAVKYVT 65
           KKVV+AFSGGLDTSF  +YLA+++G EV++   NTGGFS+E+L+  E+ AY LG   +  
Sbjct: 2   KKVVLAFSGGLDTSFCCIYLAQDRGLEVHSVIVNTGGFSDEELQEIEKRAYALGVKSHAV 61

Query: 66  LDVTQEYYEKSLKYMVFGNVLRNGTYPISVSSERIFQALAIARYANEIGADAIAHGSTGA 125
           +D T+ YYE  +KY+VFGNVL+N TYP+SVS+ER+ QA AIA Y  +IGAD +AHGSTGA
Sbjct: 62  VDETESYYEGCIKYLVFGNVLKNATYPLSVSAERVSQATAIANYVKKIGADYVAHGSTGA 121

Query: 126 GNDQIRFDMTFLVLAPNVEIITLTRDMALSRQEEIDYLNKHGFSADFTKLKYSYNVGLWG 185
           GNDQ+RFDM F +L P VEIIT  RD+ LSR+ EI+YL +HG      K +YS N GLWG
Sbjct: 122 GNDQVRFDMIFNILIPEVEIITPIRDLKLSREAEIEYLAQHGVEYSAEKARYSINKGLWG 181

Query: 186 TSICGGEILDSAQGLPETAYLKHVEKEGSEQLRLTFEKGELKAVNDETFDDPIQAIQKVE 245
           TS+ G E L S + LPE+A+   V +  S ++ LTFEKGEL A++ E    P++AIQK++
Sbjct: 182 TSVGGKETLTSHETLPESAWPTQVSETESRKVELTFEKGELVAIDGEKL-APVRAIQKLQ 240

Query: 246 EIGAAYGIGRDMHVGDTIIGIKGRVGFEAAAPMLIIGAHRFLEKYTLSKWQQYWKDQVAN 305
            I   +GIGRD+HVGDTIIGIKGRVGFEAA P+LII AH  LEK+TL+KWQ  WK+Q+++
Sbjct: 241 AIAQPFGIGRDIHVGDTIIGIKGRVGFEAAGPILIIKAHHTLEKHTLTKWQLSWKEQLSS 300

Query: 306 WYGMFLHESQYLEPVMRDIEAMLQESQRNVNGTAILELRPLSFSTVGVESEDDLVKTKFG 365
           +YG +LHE Q+ +P+MR+IEA L ++Q+ V+G   +EL P  F  +G+ES  DL+  KFG
Sbjct: 301 FYGNWLHEGQFHDPIMRNIEAFLADTQKFVSGKVFVELLPYRFQIIGIESNHDLMSNKFG 360

Query: 366 EYGEMQKGWTAEDAKGFIKVTSTPLRVYY 394
            YGEM   W+ ED KGF K+    + +++
Sbjct: 361 SYGEMNNAWSGEDVKGFSKIFGNQVMIWH 389


Lambda     K      H
   0.316    0.134    0.385 

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: 474
Number of extensions: 20
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: 402
Length of database: 395
Length adjustment: 31
Effective length of query: 371
Effective length of database: 364
Effective search space:   135044
Effective search space used:   135044
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate CA265_RS18545 CA265_RS18545 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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.aa/TIGR00032.hmm
# target sequence database:        /tmp/gapView.32306.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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-85  274.2   0.0    1.3e-85  274.1   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS18545  CA265_RS18545 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS18545  CA265_RS18545 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.1   0.0   1.3e-85   1.3e-85       1     391 [.       3     390 ..       3     393 .. 0.96

  Alignments for each domain:
  == domain 1  score: 274.1 bits;  conditional E-value: 1.3e-85
                                  TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqp.eedldaieekalklGaekayviDareefvk 66 
                                                kvvla+sGGlDts +  +l +  g+ev +v+v+ G   +e+l++ie++a +lG++ + v+D  e + +
  lcl|FitnessBrowser__Pedo557:CA265_RS18545   3 KVVLAFSGGLDTSFCCIYLAQDrGLEVHSVIVNTGGFsDEELQEIEKRAYALGVKSHAVVDETESYYE 70 
                                                8************9999998877***********987799**************************** PP

                                  TIGR00032  67 dylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpd 134
                                                  +   +  n + + +Y+ls +  R   a+++ + +kk ga+ vahG+tg GnDqvRF++++ +l p+
  lcl|FitnessBrowser__Pedo557:CA265_RS18545  71 GCIKYLVFGNVLKNATYPLSVSAERVSQATAIANYVKKIGADYVAHGSTGAGNDQVRFDMIFNILIPE 138
                                                *888899999999999**************************************************** PP

                                  TIGR00032 135 lkviaPvreleliReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvk 202
                                                +++i+P+r+l+l+Re eiey+a++G+e+ +ek   ysi++ l+g s+ ++e    + + pe ++ + +
  lcl|FitnessBrowser__Pedo557:CA265_RS18545 139 VEIITPIRDLKLSREAEIEYLAQHGVEYSAEK-ARYSINKGLWGTSVGGKETLTSHETLPESAWPTQV 205
                                                ******************************97.89**************9988888888888887766 PP

                                  TIGR00032 203 dpiektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYE 270
                                                    +   e+ +ve++FekG  va++ge+l pv  i+k++ ia   G+Gr  +v d iig+K R  +E
  lcl|FitnessBrowser__Pedo557:CA265_RS18545 206 ---SE--TESRKVELTFEKGELVAIDGEKLAPVRAIQKLQAIAQPFGIGRDIHVGDTIIGIKGRVGFE 268
                                                ...23..35679******************************************************** PP

                                  TIGR00032 271 apalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrv 338
                                                a++ +l+ikAh+ Le+ +ltk +l +ke  ++ y++ + +G ++dp + +++a++  tq+ v+G v v
  lcl|FitnessBrowser__Pedo557:CA265_RS18545 269 AAGPILIIKAHHTLEKHTLTKWQLSWKEQLSSFYGNWLHEGQFHDPIMRNIEAFLADTQKFVSGKVFV 336
                                                ******************************************************************** PP

                                  TIGR00032 339 klfkGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglqikvyre 391
                                                +l      +ig +s++ l +++  s+ + +++ + +d +Gf ki g q++++++
  lcl|FitnessBrowser__Pedo557:CA265_RS18545 337 ELLPYRFQIIGIESNHDLMSNKFGSYGEmNNAWSGEDVKGFSKIFGNQVMIWHK 390
                                                **************************987999*************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (395 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: 00:00:00.01
# Mc/sec: 8.98
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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