GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Paraburkholderia bryophila 376MFSha3.1

Align Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family

Query= TCDB::P15993
         (457 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04042 H281DRAFT_04042
           aromatic amino acid:proton symporter, AAT family
          Length = 506

 Score =  651 bits (1680), Expect = 0.0
 Identities = 318/449 (70%), Positives = 368/449 (81%), Gaps = 2/449 (0%)

Query: 5   QQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMR 64
           QQ G  LKRGLKNRHIQLIALGGAIGTGLFLGSASV+Q+AGP +ILGYAI G IAF+IMR
Sbjct: 51  QQDG--LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMR 108

Query: 65  QLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPE 124
           QLGEMV +EPVAGSFSHFAYKYWG F GF SGWNYWVLYVLV+MAELTAVG Y+ +W+P 
Sbjct: 109 QLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPG 168

Query: 125 IPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNGGPQA 184
           +PTWVSA V F  INAINL NVK +GE EFWFAIIKV+AV+ MI+FGG+LL SG+GGPQA
Sbjct: 169 VPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQA 228

Query: 185 TVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYR 244
           ++SNLW  GGF PHGF GL  M+A+IMFSFGGLEL+GITAAEAD P++SIPKA NQVIYR
Sbjct: 229 SISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYR 288

Query: 245 ILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCV 304
           ILIFYI SLAVLLSL PW  V A  SPFV+IF ++G T  AN LN+VVLTAALSVYNS V
Sbjct: 289 ILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGV 348

Query: 305 YCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMA 364
           Y NSRML+GLA+QGNAP+AL  VD+RGVP   I +SAL T  CV++NYL P  A GLLMA
Sbjct: 349 YANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMA 408

Query: 365 LVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTP 424
           LVV+ALV+NWA+ISL H+K RRA    G    F +  +P+ NWICL FMA +LVI+ MTP
Sbjct: 409 LVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILAMTP 468

Query: 425 GMAISVYLIPVWLIVLGIGYLFKEKTAKA 453
           G+++SV L+PVWL+V+  GY FK + A A
Sbjct: 469 GLSVSVLLVPVWLVVMWAGYAFKRRRAAA 497


Lambda     K      H
   0.328    0.141    0.434 

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: 775
Number of extensions: 41
Number of successful extensions: 1
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: 457
Length of database: 506
Length adjustment: 34
Effective length of query: 423
Effective length of database: 472
Effective search space:   199656
Effective search space used:   199656
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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