GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_04042 in Pseudomonas fluorescens FW300-N1B4

Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate Pf1N1B4_3559 Aromatic amino acid transport protein AroP

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559 Aromatic amino acid
           transport protein AroP
          Length = 473

 Score =  608 bits (1567), Expect = e-178
 Identities = 293/451 (64%), Positives = 354/451 (78%), Gaps = 9/451 (1%)

Query: 10  LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69
           LKRGLKNRHIQLIALGGAIGTGLFLGSA VL++AGPSMILGYAI G IAFMIMRQLGEM+
Sbjct: 11  LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMI 70

Query: 70  AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129
            +EPVAGSFSHFA+KYWG F GFLSGWN W+LY+LV M+ELTAVG Y+HYW P +PTWVS
Sbjct: 71  VEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWVS 130

Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQASISNLW 189
           A   F  IN INLANVK +GE EFWFAIIKVVA++GMI  G YLLVSG GGPQAS++NLW
Sbjct: 131 AAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGDGGPQASVTNLW 190

Query: 190 SHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIFYI 249
            HGGFFP+G  GL   +A+IMFSFGGLE++G TAAEAD+P+  IPKA+NQVIYRILIFYI
Sbjct: 191 EHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRILIFYI 250

Query: 250 CSLAVLLSLYPWNEV---------AAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYN 300
            +L VLLSL PW+ +         A  GSPFV +FS +GS   A++LN VVLTAALSVYN
Sbjct: 251 GALVVLLSLTPWDSLLTTLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLTAALSVYN 310

Query: 301 SGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGL 360
           SG Y NSRML G+AEQG+AP+AL K+D+RGVP  +I  SA  T   V++NYL+P  AL L
Sbjct: 311 SGTYCNSRMLLGMAEQGDAPKALSKIDKRGVPVRSILASAAVTLVAVLLNYLVPQHALEL 370

Query: 361 LMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILA 420
           LM+LVVA LV+NWA+IS +H K R+ M    +T +FK+ W+P  N++CLAF+  IL ++ 
Sbjct: 371 LMSLVVATLVINWAMISFSHFKFRQHMNKTKQTPLFKALWYPYGNYVCLAFVVFILGVML 430

Query: 421 MTPGLSVSVLLVPLWLVVMWAGYAFKRRRAA 451
           + PG+ +SV  +P+W+  MW  Y  K +R+A
Sbjct: 431 LIPGIQISVYAIPVWVAFMWVCYGIKNKRSA 461


Lambda     K      H
   0.327    0.140    0.440 

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: 663
Number of extensions: 26
Number of successful extensions: 3
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: 461
Length of database: 473
Length adjustment: 33
Effective length of query: 428
Effective length of database: 440
Effective search space:   188320
Effective search space used:   188320
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 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