GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Paenisporosarcina indica PN2

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 WP_075618505.1 GY23_RS06985 amino acid permease

Query= TCDB::P15993
         (457 letters)



>NCBI__GCF_001939075.1:WP_075618505.1
          Length = 452

 Score =  403 bits (1035), Expect = e-117
 Identities = 187/443 (42%), Positives = 285/443 (64%), Gaps = 2/443 (0%)

Query: 9   EQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLGE 68
           ++L RGLKNRH+QLIA+GGAIGTGLFLG+   I  AGP I+  Y + G I FLIMR LGE
Sbjct: 4   QELSRGLKNRHVQLIAIGGAIGTGLFLGAGKSIHLAGPSILFAYLLTGIICFLIMRALGE 63

Query: 69  MVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPTW 128
           +++      SF  F   Y G+ A F +GW YW  ++ +AMA+LTAVG Y QFW PE+P W
Sbjct: 64  LLLSNLKYHSFVDFVRDYLGNMAAFITGWTYWFCWISIAMADLTAVGLYTQFWLPEVPQW 123

Query: 129 VSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSG--NGGPQATV 186
           +   +  V++  +NL  VK+FGEMEFWFA+IKVIA++A+I+ G +++  G       ++ 
Sbjct: 124 MPGLIALVILLFMNLATVKLFGEMEFWFALIKVIAILALIVIGIFMIVKGFSTDAGASSF 183

Query: 187 SNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRIL 246
           +NLW  GG  P+G  G ++   +++F+F G+ELVG+TA E ++PE+ IPKA N +  RIL
Sbjct: 184 TNLWSHGGMFPNGLNGFILSFQMVVFAFVGIELVGLTAGETEDPERVIPKAINNIPIRIL 243

Query: 247 IFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVYC 306
           IFYIG+L V++S+ PW  +    SPFV +F  +G    A  +N VVLT+A S  NS ++ 
Sbjct: 244 IFYIGALIVIMSIYPWNAINPMESPFVQVFVAVGIAAAAGIVNFVVLTSAASACNSAIFS 303

Query: 307 NSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMALV 366
            SRM++ LA+  NAP  LA +    VP N +  S ++  + V++NYL PE  F L+ ++ 
Sbjct: 304 TSRMIYSLAKDKNAPVPLAKLTSGKVPSNALFFSTVIILIAVVLNYLMPEGVFTLITSIS 363

Query: 367 VSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTPGM 426
               +  W +  ++H+K+R+ + +    ++F   LYP  N++ L+F+A ++V++ +    
Sbjct: 364 TVCFIFIWGITVISHLKYRKTRPDLAKKSKFKLPLYPFSNYLILVFLAFIIVVLALAEDT 423

Query: 427 AISVYLIPVWLIVLGIGYLFKEK 449
            I++++ PVW I+L + Y  +EK
Sbjct: 424 RIALFITPVWFILLILIYKMREK 446


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: 564
Number of extensions: 27
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: 457
Length of database: 452
Length adjustment: 33
Effective length of query: 424
Effective length of database: 419
Effective search space:   177656
Effective search space used:   177656
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 24 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