GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_0927
          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 (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