GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagP in Gallaecimonas xiamenensis 3-C-1

Align N-acetylglucosamine transporter nagP (characterized)
to candidate WP_156804425.1 B3C1_RS01975 glucose/galactose MFS transporter

Query= reanno::ANA3:7025962
         (432 letters)



>NCBI__GCF_000299915.1:WP_156804425.1
          Length = 421

 Score =  409 bits (1051), Expect = e-119
 Identities = 217/425 (51%), Positives = 284/425 (66%), Gaps = 12/425 (2%)

Query: 15  MAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVIRK 74
           MAI+  LFFI GF TWLNGSL+P+LK + QLN FQA  + F+FYIA T  ALP A ++ +
Sbjct: 1   MAIIGLLFFIFGFVTWLNGSLIPFLKIVCQLNDFQALFVAFAFYIAYTVMALPMAALLER 60

Query: 75  VGYKNGMALGMGIMMLAGLLFIPAAKTQIFGLFLCAQLVMGTGQTLLQTAVNPYVVRLGP 134
           +GY+NGMA G+ IM    LLFIPAA +  +GLFL A  V+G+G TLLQTA NPYVV LGP
Sbjct: 61  LGYRNGMAWGLAIMAAGALLFIPAALSAQYGLFLLALFVLGSGLTLLQTASNPYVVLLGP 120

Query: 135 EESAAARVSVMGILNKGAGVIAPLVFSALILDSFKD-------RIGTTLTQVQIDEMANS 187
            ESAA R+S+MGI+NK AGV+ PL+F++L+L             +   +   Q+D +A  
Sbjct: 121 AESAAMRISIMGIINKTAGVLVPLLFTSLVLSDLAQVNQASLAHLDPAVRDAQLDAVAER 180

Query: 188 LVFPYLGMAIFIGVLALAVKKSPLPELSNEDEVAEHTDKGQIKAALSHPNLAFGVIALFV 247
           LV PYL MA  +  L   V+ SPLPE++ + E      KG++   L +P L  G + LF 
Sbjct: 181 LVLPYLYMAAALMALIALVRLSPLPEIAPQGE----GGKGRLAELLRYPQLILGALTLFA 236

Query: 248 YVAVEVIAGDTIGTFALSLGVEHYGVMTSYTMVCMVLGYTLGIILIPRFISQPTALMISA 307
           +V +EVIA DTIG     LGV  +  +TSYTMV MVLGY LG++LIPR++SQ  AL+ S 
Sbjct: 237 FVGLEVIAADTIGLLGEKLGVARFASLTSYTMVFMVLGYGLGVVLIPRWLSQSRALLYSG 296

Query: 308 ILGLLLTLAILFGDNNSYAIANALLVPFGGVALPDTLLFIAFLGLANAIVWPAVWPLALS 367
           + G+   LA+LF    S A+++ L        +PD +LF+A +GLA+A+VWPAVWPLAL 
Sbjct: 297 LAGVAAVLAVLFSSPGSQALSSFLWGWTPIPTVPDPVLFVALMGLAHALVWPAVWPLALD 356

Query: 368 GLGKLTSTGSALLIMGIAGGAFGPLFWGLTSSATDMGQQGGYMVMLPCYLFILFYAVKGH 427
           GLG+ T+ GSALLIMGIAGGA  PL +G  + +    QQ  Y++ LPCYL I FYA+KGH
Sbjct: 357 GLGRHTAQGSALLIMGIAGGALLPLAFGHLAESLGSIQQ-AYVLALPCYLLIAFYALKGH 415

Query: 428 KMRHW 432
           +MR W
Sbjct: 416 RMRRW 420


Lambda     K      H
   0.327    0.141    0.421 

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: 630
Number of extensions: 35
Number of successful extensions: 5
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: 432
Length of database: 421
Length adjustment: 32
Effective length of query: 400
Effective length of database: 389
Effective search space:   155600
Effective search space used:   155600
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