GapMind for catabolism of small carbon sources

 

Aligments for a candidate for permease in Pseudomonas putida KT2440

Align histidine permease (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein

Query= reanno::pseudo3_N2E3:AO353_12275
         (468 letters)



>lcl|FitnessBrowser__Putida:PP_0927 PP_0927 aromatic amino acid
           transport protein
          Length = 453

 Score =  378 bits (971), Expect = e-109
 Identities = 199/449 (44%), Positives = 279/449 (62%), Gaps = 14/449 (3%)

Query: 2   QKPANGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMR 61
           Q     L+RGL  RHI+ +ALG AIGTGLF G A  IQ+AGP+VLL Y I G   F++MR
Sbjct: 4   QSTPERLQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFLIMR 63

Query: 62  ALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPE 121
            LGEM V  PVAGSF  +A  Y    AGF+ GW Y    V+VGMA++TA GIY+ +W+P+
Sbjct: 64  QLGEMVVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPD 123

Query: 122 VSRWIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPG 181
              W        ++  +NL  VKV+GEMEFW +L+KV AIV+MI  GFG  L G S   G
Sbjct: 124 FPTWATAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMI--GFGAWLLG-SGHGG 180

Query: 182 QVTDISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAV 241
               ++NLW  GGF PNG+ GL+ + AV+MF+FGG+E++G+TA EA +P+  +P+A N V
Sbjct: 181 PDASVANLWQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQV 240

Query: 242 PLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAIN 301
             RIL+FY+  + VL+S++PWQ++   GSPFV IF +L     ATILNIVV+TAA+S  N
Sbjct: 241 VYRILIFYIGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIVVLTAALSVYN 300

Query: 302 SDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLL 361
           S ++   RM+FGLA QG AP+    +SR+GVP   + V + A  L VL+NYL+P   F L
Sbjct: 301 SCVYANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPGGAFGL 360

Query: 362 IASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFW-----PYAPMAAIAFMLF 416
           + ++A  A V  W  I  T +  R++  A  +       PF+     P      +AF++ 
Sbjct: 361 LMALAVSALVINWASISITHLKFRKAKLAAGI------TPFYKSLGHPLTNYLCLAFIVL 414

Query: 417 VFGVLGYFPDTQAALIVGVVWIVLLVLAY 445
           +  V+   P  + ++++   WI +L +A+
Sbjct: 415 ILVVMYLTPPIRISVMLIPAWIAVLWVAF 443


Lambda     K      H
   0.329    0.142    0.441 

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: 634
Number of extensions: 29
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: 468
Length of database: 453
Length adjustment: 33
Effective length of query: 435
Effective length of database: 420
Effective search space:   182700
Effective search space used:   182700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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