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

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.7155.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.00
//
[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:

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis