GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS17540 in Pseudomonas fluorescens GW456-L13

Align Amino acid permease-associated region (characterized, see rationale)
to candidate PfGW456L13_3582 Aspartate-proton symporter

Query= uniprot:B2SZ32
         (555 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3582
          Length = 548

 Score =  372 bits (954), Expect = e-107
 Identities = 202/540 (37%), Positives = 311/540 (57%), Gaps = 19/540 (3%)

Query: 26  KSSIQRNIGPFALMLTGLGSIIGSGWLFGAWKAAKIAGPAAVCAWVIGAVVILAIALTYA 85
           +   ++ +    L   GLG+I GSGWLF A   + IAGPA + +W++G   +L + + Y 
Sbjct: 4   QGKFKKQLSLIDLTFIGLGAIFGSGWLFAASHVSAIAGPAGIFSWLLGGFAVLLLGIVYC 63

Query: 86  ELGAMFPESGGMVRYARYSHGALVGFISAWANWIAIVSVIPIEAEASIQYMSTWPYPWAH 145
           ELGA  P +GG+VRY  YSHG L+G++  +   IA  S++ IE  A+ QY + W +P   
Sbjct: 64  ELGAALPRAGGVVRYPVYSHGPLLGYLMGFITLIAFSSLVAIEVVAARQYAAAW-FP--- 119

Query: 146 ALFVDGSL--TTNGLLLSAALVIIYFMLNYWGVKLFARANSAITIFKFLIPGATILGLMF 203
           AL   GS   T  G L+   L+ ++FMLNY+ VK FA+AN+ I++FKF++P   ++G++F
Sbjct: 120 ALTQAGSSNPTAIGWLVQFGLLCLFFMLNYYSVKTFAKANNLISMFKFIVP-LLVIGVLF 178

Query: 204 AGFHKENFGEASTFAPYGWSAVLTAVSTSGIVFAFNGFQSPINLAGEARNPAKSVPFAVI 263
             F  ENF ++  F P+G S V  AVS  GI+FA+ G    I++A E +NP +++P A+I
Sbjct: 179 TFFKPENF-QSQGFMPFGLSGVEMAVSAGGIIFAYLGLTPIISVASEVKNPQRTIPIALI 237

Query: 264 GSILLALVIYVLLQIAYIGAVNPSDVMKGWSHF--NFASPFAELAIALNLNWLAILLYVD 321
            S+LL+  IYVLLQ+A++G V    +  GW+      A P+ ++A+AL + WLA L+  D
Sbjct: 238 LSVLLSTAIYVLLQVAFLGGVPTEMLANGWAGVAKELALPYRDIALALGVGWLAYLVVAD 297

Query: 322 AFVSPSGTGTTYMATTSRMIYAMERNNTMPKMFGNVHPFYGVPRQAMWFNLLVSFIFLFF 381
           A +SPSG G  YM  T R+IY   +  T  K+F  +    G+PR A+W    +S  +   
Sbjct: 298 AVISPSGCGNIYMNATPRVIYGWAQTGTFFKVFTRIDEKSGIPRPALWLTFALSVFWTLP 357

Query: 382 FRGWSSLAAVISVATVISYLTGPISLMALRRAATDLERPLHIPGMKIIAPFAFVCASLIL 441
           F  W +L  V+S A V+SY   P+S+ ALRR A D+ RP  +  M ++ P +F+ A+LI+
Sbjct: 358 FPSWEALINVVSAALVLSYAVAPVSVAALRRNAPDMPRPFKVKRMGVLGPVSFIIAALIV 417

Query: 442 YWAKWPLTGEIILLMVVALPVYFYFQ--AKSGFAGWGRDLKAAWWLVAYLPVMAILSLIG 499
           YW+ W     ++ L ++   VY        +      + ++++ WL+ +  V  +LS +G
Sbjct: 418 YWSGWSTVSWLLGLQILMFVVYLLCGRFVPTQHLSLAQQVRSSAWLIGFYAVTIVLSWLG 477

Query: 500 SKQFGGHDLIPYGWDMVVVIAFSLVFYYWGVTSG-----YRSEYLDERSEHDEVLEGMGA 554
           S  FGG  ++ + +D VVV A ++  YYWG  +G      R E  D  S+ D V  G  A
Sbjct: 478 S--FGGMGVLTHPFDTVVVAACAMGIYYWGAATGVPAHLVRLEDEDGESQADPVHTGTTA 535


Lambda     K      H
   0.326    0.139    0.445 

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: 1042
Number of extensions: 67
Number of successful extensions: 6
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: 555
Length of database: 548
Length adjustment: 36
Effective length of query: 519
Effective length of database: 512
Effective search space:   265728
Effective search space used:   265728
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: 53 (25.0 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